Contacts of the helix formed by residues 499 - 519 (chain C) in PDB entry 6NR8
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 499 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ILE* 5.8 1.3 - - + +
137C LEU* 3.5 43.4 - - + +
138C LYS* 3.9 15.7 - - + +
141C SER* 3.4 17.0 - - - +
404C ASP* 3.2 28.4 + - - +
406C GLN* 2.9 38.2 + - - +
408C VAL* 4.1 10.0 - - - +
497C GLU 3.9 0.2 + - - -
498C PRO* 1.3 73.1 - - - +
500C ALA* 1.3 59.7 + - - +
502C LYS* 3.3 3.6 + - - +
503C LEU* 3.0 33.7 + - + +
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Residues in contact with ALA 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C ASN* 3.9 17.7 - - + +
403C LEU* 3.7 29.2 - - + -
404C ASP* 3.8 20.7 - - + +
498C PRO* 3.2 1.4 - - - +
499C LEU* 1.3 82.8 - - - +
501C VAL* 1.3 61.0 + - - +
503C LEU* 3.4 6.4 + - - +
504C GLN* 3.2 31.6 + - - +
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Residues in contact with VAL 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLN* 5.2 2.6 + - - +
91C VAL* 4.7 17.0 - - + -
93C ASP* 4.7 16.6 - - + +
94C GLY* 5.4 1.6 - - - +
400C ASN* 3.9 23.4 - - - +
497C GLU* 4.1 20.2 - - + +
498C PRO* 3.3 31.4 - - + +
500C ALA* 1.3 79.1 - - - +
502C LYS* 1.3 60.8 + - - +
504C GLN* 4.7 3.5 - - - +
505C THR* 2.6 38.3 + - - +
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Residues in contact with LYS 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C MET* 3.7 9.8 - - + +
137C LEU* 3.7 23.1 - - + -
408C VAL* 3.9 17.9 - - + -
409C PRO 5.2 0.4 + - - -
410C GLY* 5.9 0.8 - - - -
411C GLY 5.0 4.2 + - - -
414C SER* 3.5 27.2 + - - +
415C GLU* 3.0 29.5 + - - +
447C ILE* 6.2 1.4 - - - +
497C GLU* 3.3 25.0 + - - +
498C PRO 3.7 0.6 + - - +
499C LEU 3.3 8.2 + - - +
500C ALA 3.2 0.4 - - - -
501C VAL* 1.3 82.3 - - - +
503C LEU* 1.3 63.0 + - - +
505C THR* 3.8 5.4 - - + -
506C TYR* 3.2 21.2 + - + +
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Residues in contact with LEU 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LEU* 4.9 9.0 - - + -
133C MET* 3.8 11.0 - - - -
134C ILE* 3.7 37.9 - - + -
137C LEU* 3.7 21.3 - - + -
499C LEU* 3.0 25.5 + - + +
500C ALA* 3.9 7.0 - - - +
501C VAL 3.4 0.2 - - - -
502C LYS* 1.3 78.5 - - - +
504C GLN* 1.3 56.7 + - + +
506C TYR* 3.0 4.5 + - - +
507C LYS* 2.6 44.3 + - + +
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Residues in contact with GLN 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLN* 3.7 6.7 - - - +
90C GLU* 3.7 18.3 + - - +
91C VAL* 3.4 26.9 - - - +
400C ASN* 4.9 1.0 + - - -
403C LEU* 3.5 28.8 - - - +
500C ALA* 3.2 17.4 + - - +
501C VAL* 4.7 1.5 - - - +
503C LEU* 1.3 78.2 - - + +
505C THR* 1.3 58.0 + - - +
507C LYS* 3.4 28.3 + - + +
508C THR* 2.6 37.6 + - - -
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Residues in contact with THR 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLN* 4.0 9.8 + - - +
94C GLY* 4.3 11.0 - - - +
97C SER* 4.0 27.4 - - - +
98C VAL* 3.6 29.3 - - + +
101C LEU* 4.3 10.7 - - + +
501C VAL* 2.6 26.9 + - - +
502C LYS* 3.8 7.9 - - + -
503C LEU 3.2 0.4 - - - -
504C GLN* 1.3 78.4 - - - +
506C TYR* 1.3 60.1 - - - +
508C THR 3.5 0.2 + - - -
509C ALA* 3.3 19.9 + - - +
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Residues in contact with TYR 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 4.6 10.8 - - + -
105C MET* 4.1 20.9 - - + -
129C ALA* 2.7 46.3 + - - +
130C LEU* 3.6 28.2 + - + -
133C MET* 3.5 37.9 - - + -
418C VAL* 5.9 0.9 - - + -
422C LEU* 5.2 1.7 - - - +
440C VAL* 4.1 8.1 - - + +
444C LEU* 3.9 29.6 - - + -
502C LYS* 3.2 12.3 + - + +
503C LEU 3.0 7.0 + - - +
505C THR* 1.3 77.9 - - - +
507C LYS* 1.3 61.0 + - - +
509C ALA* 3.2 4.2 + - - +
510C VAL* 3.0 36.4 + - + +
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Residues in contact with LYS 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLU* 4.2 13.4 + - - -
130C LEU* 4.1 28.0 - - + -
503C LEU* 2.6 28.7 + - + +
504C GLN* 3.4 36.6 + - + +
505C THR 3.3 0.2 - - - -
506C TYR* 1.3 73.3 - - - +
508C THR* 1.3 64.1 + - - +
510C VAL* 3.5 3.7 + - - +
511C GLU* 3.1 24.3 + - - +
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Residues in contact with THR 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ILE* 3.6 37.9 - - + +
86C THR* 5.0 7.3 - - + +
87C GLN* 2.9 14.3 + - + +
90C GLU* 3.8 5.7 + - - -
98C VAL* 3.8 23.6 - - + -
504C GLN 2.6 21.8 + - - -
507C LYS* 1.3 80.6 + - - +
509C ALA* 1.3 57.3 + - - +
511C GLU* 3.1 16.3 + - - +
512C THR* 3.0 31.8 + - - -
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Residues in contact with ALA 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C VAL 3.8 16.1 + - - +
101C LEU* 3.8 20.4 - - + -
102C ALA* 4.0 10.5 - - - +
105C MET* 3.3 32.9 - - + +
505C THR 3.3 10.1 + - - +
506C TYR* 3.2 8.8 + - - +
508C THR* 1.3 75.4 - - - +
510C VAL* 1.3 64.6 + - - +
512C THR* 4.1 1.6 - - - -
513C ALA 3.2 16.5 + - - -
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Residues in contact with VAL 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C MET* 4.6 7.9 - - + -
126C TYR* 3.6 25.6 - - + +
127C ARG* 5.4 5.8 - - - +
129C ALA* 5.7 0.9 - - + -
130C LEU* 3.9 24.0 - - + -
506C TYR* 3.0 51.3 + - + +
507C LYS 3.7 8.7 - - - +
509C ALA* 1.3 76.8 - - - +
511C GLU* 1.3 62.6 + - - +
513C ALA* 3.3 3.1 + - - +
514C VAL* 3.1 33.4 + - + +
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Residues in contact with GLU 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ILE* 5.1 12.0 - - + +
86C THR* 4.7 17.1 + - - +
507C LYS* 3.1 14.2 + - - +
508C THR* 3.1 19.2 + - - +
510C VAL* 1.3 77.3 - - - +
512C THR* 1.3 59.0 + - - +
514C VAL* 4.0 5.2 - - - +
515C LEU* 3.1 29.6 + - + +
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Residues in contact with THR 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C SER* 5.6 1.6 - - - +
80C MET* 3.8 29.2 - - - -
83C ILE* 3.3 36.6 - - + +
102C ALA* 4.0 20.2 - - + -
106C LEU* 4.3 1.3 - - + +
508C THR 3.0 16.0 + - - -
509C ALA* 4.1 0.6 - - - -
511C GLU* 1.3 74.3 - - - +
513C ALA* 1.3 66.3 + - - +
515C LEU* 3.1 9.2 + - + +
516C LEU* 3.1 35.8 + - + +
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Residues in contact with ALA 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ALA* 5.0 3.3 - - - +
105C MET* 3.7 25.6 - - + -
106C LEU* 3.4 21.2 - - + +
126C TYR* 3.6 24.1 - - + -
509C ALA 3.2 16.6 + - - +
510C VAL* 3.3 3.8 + - - +
512C THR* 1.3 77.0 - - - +
514C VAL* 1.3 63.0 + - - +
517C LEU* 3.3 23.2 + - - +
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Residues in contact with VAL 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ILE* 4.0 31.4 - - + +
126C TYR* 3.7 31.0 - - + -
127C ARG* 5.5 5.8 - - - +
510C VAL* 3.1 23.5 + - + +
511C GLU* 4.0 5.4 - - - +
513C ALA* 1.3 74.4 - - - +
515C LEU* 1.3 66.1 + - - +
517C LEU* 3.4 5.8 + - - +
518C ARG* 3.4 30.5 + - - +
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Residues in contact with LEU 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 6.1 0.9 - - - +
44A MET* 6.2 0.9 - - + -
54A ILE* 4.7 22.4 - - + -
79C SER* 4.4 23.3 - - - +
83C ILE* 4.8 17.0 - - + -
511C GLU* 3.1 21.2 + - + +
512C THR* 3.1 9.6 + - + +
514C VAL* 1.3 77.6 - - - +
516C LEU* 1.3 71.3 + - + +
518C ARG* 3.1 25.6 + - + +
519C ILE* 3.3 14.4 - - + +
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Residues in contact with LEU 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A MET* 4.0 17.3 - - + -
23C GLN* 5.7 0.5 - - - +
26C ASN* 3.7 28.5 + - + +
30C ALA* 4.6 11.4 - - + -
76C ALA* 3.8 35.2 - - + +
79C SER* 4.9 3.1 - - - -
80C MET* 4.6 5.8 - - - -
106C LEU* 3.7 26.2 - - + -
110C GLU* 5.2 4.3 - - - +
512C THR* 3.1 24.3 + - + +
515C LEU* 1.3 86.7 - - + +
517C LEU* 1.3 63.4 + - - +
518C ARG 3.2 0.2 - - - -
519C ILE* 3.2 27.4 + - + +
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Residues in contact with LEU 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.9 0.8 - - - +
23C GLN* 6.1 1.1 - - - +
106C LEU* 4.5 7.1 - - + +
110C GLU* 4.9 15.3 - - + +
114C GLU* 4.0 29.4 - - + +
119C PRO* 3.5 34.5 - - + +
122C VAL* 3.7 28.3 - - + -
123C ILE* 3.6 18.2 - - + +
126C TYR* 4.0 11.4 - - + -
513C ALA 3.3 17.4 + - - +
514C VAL 3.6 5.2 - - - +
515C LEU 3.2 0.8 - - - -
516C LEU* 1.3 78.2 - - - +
518C ARG* 1.3 60.4 + - - +
519C ILE 3.4 0.3 + - - -
520C ASP* 3.8 14.6 - - - +
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Residues in contact with ARG 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PRO 5.3 3.8 + - - -
40A GLY 3.0 26.9 + - - -
41A LEU* 3.4 24.2 - - + +
42A ASP* 3.0 74.0 + - + +
43A LYS* 3.1 20.4 + - - -
56A ASN* 3.4 9.3 - - - +
123C ILE* 4.6 13.2 - - + +
514C VAL* 3.4 23.9 + - - +
515C LEU* 3.1 17.1 + - + +
517C LEU* 1.3 77.5 - - - +
519C ILE* 1.3 58.2 + - + +
520C ASP* 4.3 0.8 - - - -
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Residues in contact with ILE 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP 3.4 19.5 - - - +
44A MET* 3.7 47.8 - - + +
54A ILE* 3.7 24.0 - - + -
22C VAL* 3.7 12.4 - - + +
23C GLN* 4.1 3.3 - - - +
26C ASN* 3.1 31.4 + - - +
515C LEU* 3.3 20.0 - - + +
516C LEU* 3.2 17.8 + - + +
517C LEU 3.2 1.6 - - - -
518C ARG* 1.3 73.3 - - + +
520C ASP* 1.3 67.9 + - - +
521C ASP 4.1 3.1 - - - +
522C ILE* 4.0 4.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il