Contacts of the helix formed by residues 494 - 508 (chain C) in PDB entry 6RI7
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 ASN 494 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471C VAL* 4.0 8.4 - - + +
493C ILE* 1.3 80.3 - - - +
495C ALA* 1.3 65.1 + - - +
496C LYS* 2.9 39.7 + - - +
497C PRO* 3.0 29.9 - - + +
498C ILE* 3.2 13.3 - - - +
30T C 5.4 3.6 + - - -
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Residues in contact with ALA 495 (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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123C TYR* 4.4 7.0 - - + +
124C MET* 3.3 40.8 - - - +
125C GLY* 3.6 7.6 - - - +
493C ILE* 4.2 2.8 - - - +
494C ASN* 1.3 75.2 + - - +
496C LYS* 1.3 66.1 + - - +
498C ILE* 2.7 25.4 + - - +
499C SER* 2.9 12.5 + - - -
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Residues in contact with LYS 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C ASN* 2.9 31.1 + - - +
495C ALA* 1.3 77.6 - - - +
497C PRO* 1.3 58.8 - - + +
499C SER* 3.5 7.4 + - - -
500C ALA* 2.9 30.0 + - + +
29T A 2.6 58.5 + - - +
30T C 4.6 3.7 + - - -
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Residues in contact with PRO 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C GLY* 5.6 1.6 - - - -
470C ARG* 4.9 17.5 - - + -
471C VAL* 5.3 8.1 - - + -
494C ASN* 3.0 41.7 - - + +
496C LYS* 1.3 86.6 - - + +
498C ILE* 1.3 64.7 + - + +
500C ALA* 3.1 7.4 + - + +
501C ALA* 2.9 25.1 + - - +
29T A 4.7 12.3 - - - +
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Residues in contact with ILE 498 (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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124C MET* 4.3 21.5 - - + +
127C ILE* 6.0 0.9 - - + -
464C PHE* 3.8 34.8 - - + -
467C GLY* 4.1 22.9 - - - +
468C LEU* 4.3 14.1 - - + -
471C VAL* 3.8 22.2 - - + -
493C ILE* 5.6 3.1 - - + -
494C ASN 3.2 25.6 - - - +
495C ALA* 2.7 17.4 + - - +
497C PRO* 1.3 71.6 - - + +
499C SER* 1.3 64.9 + - - +
501C ALA* 3.2 7.1 + - - +
502C VAL* 3.0 27.3 + - + +
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Residues in contact with SER 499 (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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124C MET 5.0 1.7 + - - -
125C GLY* 4.9 13.7 - - - -
126C GLU 4.8 10.9 + - - +
495C ALA* 2.9 11.7 + - - -
496C LYS* 3.7 11.2 - - - -
498C ILE* 1.3 76.9 - - - +
500C ALA* 1.3 58.6 + - - +
502C VAL* 3.1 9.5 - - - +
503C LYS* 2.8 37.4 + - - +
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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
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496C LYS* 2.9 20.5 + - + +
497C PRO* 3.5 8.3 - - + +
499C SER* 1.3 77.0 - - - +
501C ALA* 1.3 58.7 + - - +
503C LYS* 3.3 6.1 + - - +
504C GLU* 2.9 31.8 + - - +
28T G 5.9 7.0 - - - +
29T A 5.1 7.4 - - - +
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Residues in contact with ALA 501 (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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463C GLN* 4.6 18.6 + - - +
466C VAL* 5.8 2.2 - - + -
467C GLY* 4.5 21.1 - - - +
470C ARG* 5.8 7.9 - - + +
497C PRO 2.9 16.1 + - - +
498C ILE 3.7 3.6 - - - +
500C ALA* 1.3 78.7 - - - +
502C VAL* 1.3 64.8 + - - +
504C GLU* 3.2 7.3 + - - +
505C PHE* 2.9 21.9 + - - +
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Residues in contact with VAL 502 (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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126C GLU 4.5 7.4 - - - +
127C ILE* 4.3 27.6 - - + -
128C PRO* 4.6 3.6 - - + -
460C ALA* 6.5 1.8 - - + -
463C GLN* 5.2 4.9 - - + +
464C PHE* 5.3 14.8 - - + +
498C ILE* 3.0 16.2 + - + +
499C SER* 3.1 18.4 - - - +
501C ALA* 1.3 77.5 - - - +
503C LYS* 1.3 65.8 + - - +
505C PHE* 3.2 8.1 + - + +
506C PHE* 3.0 47.5 + - + +
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Residues in contact with LYS 503 (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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91C THR* 4.2 25.0 - - + +
138C ILE* 4.9 10.7 - - + +
139C ASN* 4.8 10.3 + - - +
499C SER* 2.8 24.1 + - - +
500C ALA* 3.4 7.4 - - - +
502C VAL* 1.3 80.3 - - + +
504C GLU* 1.3 63.4 + - - +
506C PHE* 3.4 2.3 + - - +
507C GLY* 2.9 22.7 + - - -
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Residues in contact with GLU 504 (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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500C ALA 2.9 18.2 + - - +
501C ALA* 3.7 6.3 - - - +
503C LYS* 1.3 76.2 - - - +
505C PHE* 1.3 64.1 + - - +
507C GLY* 5.0 0.4 - - - -
508C SER* 2.9 40.1 + - - +
320D ASN* 2.7 34.1 + - - +
321D LYS* 4.8 9.4 - - - +
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Residues in contact with PHE 505 (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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145C ILE* 5.2 7.4 - - + -
459C MET* 3.4 48.2 - - + -
460C ALA* 4.7 2.0 - - - -
463C GLN* 4.0 37.2 - - + +
501C ALA 2.9 14.6 + - - +
502C VAL* 3.5 11.0 - - + +
503C LYS 3.2 0.2 - - - -
504C GLU* 1.3 80.2 - - - +
506C PHE* 1.3 105.4 + + - +
507C GLY 3.0 1.6 + - - -
508C SER 3.3 13.1 + - - +
509C SER* 3.8 17.7 - - - -
511C LEU* 5.3 8.1 - - + -
512C SER* 3.6 11.0 - - - -
535C PRO* 5.6 7.4 - - + -
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Residues in contact with PHE 506 (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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35C PHE* 5.5 3.4 - + - -
127C ILE* 5.7 0.2 - - + -
128C PRO* 3.2 44.9 - - + -
136C PHE* 4.5 11.9 - + + -
138C ILE* 3.6 29.7 - - + +
145C ILE* 4.1 25.8 - - + -
456C VAL* 4.6 13.5 - - + -
460C ALA* 4.6 18.4 - - + -
502C VAL* 3.0 22.9 + - + +
503C LYS* 4.3 2.2 - - - +
505C PHE* 1.3 110.8 - + - +
507C GLY* 1.3 54.4 + - - +
512C SER* 2.2 26.5 + - - -
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Residues in contact with GLY 507 (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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138C ILE* 4.6 9.6 - - - +
143C ARG* 2.2 45.6 + - - -
503C LYS 2.9 17.3 + - - -
504C GLU* 4.5 0.4 - - - -
506C PHE* 1.3 79.1 - - - +
508C SER* 1.3 61.9 + - - +
512C SER* 3.8 0.4 - - - -
25T C 4.8 8.9 - - - +
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Residues in contact with SER 508 (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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143C ARG* 4.6 0.4 - - - +
504C GLU* 2.9 33.9 + - - +
505C PHE* 3.3 3.7 - - - +
507C GLY* 1.3 72.7 + - - -
509C SER* 1.3 64.5 - - - +
25T C 4.0 22.0 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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