Contacts of the helix formed by residues 114 - 133 (chain I) 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 PRO 114 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I VAL* 3.4 45.7 - - + +
111I LYS* 3.5 25.5 - - + -
113I HIS* 1.3 100.3 - - + +
115I THR* 1.3 67.1 + - + +
116I SER 3.2 1.6 + - - -
117I VAL* 4.0 4.0 + - + +
118I ILE* 4.3 1.4 - - - +
52L LEU* 4.5 14.6 - - + +
54L PRO* 4.1 9.0 - - + +
55L LYS* 3.7 30.3 - - + -
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Residues in contact with THR 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113I HIS* 3.2 28.8 + - + -
114I PRO* 1.3 79.1 - - + +
116I SER* 1.3 54.0 + - - +
117I VAL 3.2 2.0 - - - -
118I ILE* 3.0 13.0 + - + -
119I SER* 2.4 44.2 + - - -
54L PRO* 3.7 32.1 - - + -
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Residues in contact with SER 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I ILE* 5.9 2.0 - - - +
113I HIS* 3.3 26.8 + - - +
114I PRO 3.2 1.6 - - - -
115I THR* 1.3 76.1 + - - +
117I VAL* 1.3 60.5 + - - +
119I SER* 4.0 6.9 - - - -
120I GLY* 2.7 28.2 + - - -
433I ARG* 5.7 4.5 - - - -
434I GLU* 3.4 39.0 + - - +
497L LYS 5.1 2.3 + - - -
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Residues in contact with VAL 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I LEU* 3.4 49.6 - - + +
108I VAL* 3.7 18.2 - - + +
111I LYS* 6.4 0.9 - - - -
113I HIS 5.7 0.9 - - - +
114I PRO 4.0 2.7 + - - +
115I THR 3.2 0.4 - - - -
116I SER* 1.3 77.3 - - - +
118I ILE* 1.3 59.1 + - - +
120I GLY 3.3 0.5 + - - -
121I TYR* 2.9 63.0 + - + +
433I ARG* 4.7 15.9 - - + +
434I GLU* 5.4 0.4 - - - +
437I ALA* 3.4 19.4 - - + +
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Residues in contact with ILE 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I VAL* 4.3 6.7 - - + -
114I PRO 4.3 5.6 - - - +
115I THR* 3.0 23.5 + - + +
117I VAL* 1.3 75.2 - - - +
119I SER* 1.3 60.0 + - - +
121I TYR* 3.0 28.0 + - + +
122I ARG* 2.9 30.9 + - + +
522I ILE* 3.7 41.5 - - + +
525I LEU* 3.6 29.4 - - + -
54L PRO* 4.9 11.4 - - + -
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Residues in contact with SER 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I THR* 2.4 39.7 + - - -
116I SER* 4.0 7.8 - - - -
118I ILE* 1.3 66.1 - - - +
120I GLY* 1.3 56.1 + - - +
122I ARG* 3.5 9.0 - - - +
123I LEU* 2.6 37.4 + - - +
126I LYS* 5.1 0.3 + - - -
434I GLU* 6.1 0.4 - - - -
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Residues in contact with GLY 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I SER 2.7 21.8 + - - -
117I VAL 3.3 4.0 + - - -
118I ILE 3.2 0.2 - - - -
119I SER* 1.3 74.0 - - - +
121I TYR* 1.3 56.4 + - - +
123I LEU* 4.3 7.2 - - - -
124I ALA* 3.1 21.7 + - - +
434I GLU* 4.5 8.7 - - - +
437I ALA* 3.8 15.3 - - - -
438I ILE* 3.3 19.5 + - - +
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Residues in contact with TYR 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100I LEU* 4.4 9.3 + - + -
103I ASN* 3.9 8.2 + - + +
104I ALA* 3.3 37.2 + - + +
107I LEU* 5.0 1.4 - - - +
117I VAL* 2.9 35.4 + - + +
118I ILE* 3.0 35.8 + - + +
120I GLY* 1.3 78.1 - - - +
122I ARG* 1.3 57.6 + - - +
124I ALA* 3.4 7.1 + - - +
125I CYS* 2.8 26.2 + - - +
436I LEU 5.1 0.7 - - - -
437I ALA* 3.2 33.6 - - - -
440I GLU* 5.7 1.7 - - + +
441I PHE* 4.5 19.5 - + + -
518I THR* 3.7 25.3 + - + +
521I ALA* 5.0 9.0 - - + -
522I ILE* 4.7 7.2 - - + -
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Residues in contact with ARG 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I ILE* 2.9 25.1 + - + +
119I SER* 3.1 9.8 + - - +
121I TYR* 1.3 73.4 - - - +
123I LEU* 1.3 57.0 + - - +
125I CYS* 3.1 32.1 + - - +
126I LYS* 2.7 57.7 + - - +
515I LYS* 4.1 29.1 + - - +
518I THR* 4.0 19.5 - - - -
519I GLU* 5.6 0.6 - - - +
522I ILE* 4.4 9.2 - - + +
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Residues in contact with LEU 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I SER 2.6 22.0 + - - +
120I GLY* 4.1 6.7 - - - +
122I ARG* 1.3 72.5 - - - +
124I ALA* 1.3 52.2 + - - +
126I LYS* 3.3 18.5 + - - +
127I GLU* 2.8 35.4 + - - +
130I ARG* 4.5 9.2 - - - +
426I TYR* 3.5 30.5 - - + +
430I MET* 3.8 30.5 - - + -
434I GLU* 6.1 2.9 - - + -
438I ILE* 4.1 9.0 - - + -
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Residues in contact with ALA 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120I GLY 3.1 20.9 + - - +
121I TYR 3.5 5.4 - - - +
123I LEU* 1.3 75.2 - - - +
125I CYS* 1.3 62.5 + - - +
127I GLU* 3.5 2.9 + - - -
128I ALA* 3.2 18.9 + - - +
423I LEU* 3.3 17.8 - - + +
438I ILE* 3.7 27.3 - - + +
441I PHE* 3.6 28.0 - - + -
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Residues in contact with CYS 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I TYR 2.8 15.1 + - - +
122I ARG* 3.1 40.1 + - - +
124I ALA* 1.3 76.4 - - - +
126I LYS* 1.3 62.7 + - + +
128I ALA* 3.4 7.8 + - - +
129I VAL* 3.3 33.0 + - - +
441I PHE* 4.6 5.4 - - + -
511I VAL 5.2 0.2 - - - -
514I LEU* 4.1 31.2 - - - -
515I LYS* 4.6 7.2 - - - -
518I THR* 4.4 7.4 - - - +
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Residues in contact with LYS 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I SER 5.1 0.4 + - - -
122I ARG* 2.7 33.1 + - + +
123I LEU* 3.4 38.8 - - + +
125I CYS* 1.3 72.6 - - + +
127I GLU* 1.3 65.9 + - - +
129I VAL* 3.5 8.8 + - + +
130I ARG* 3.1 44.3 + - - +
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Residues in contact with GLU 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123I LEU 2.8 18.8 + - - +
124I ALA* 3.8 5.8 - - - +
125I CYS 3.3 0.2 - - - -
126I LYS* 1.3 74.7 - - - +
128I ALA* 1.3 65.7 + - - +
130I ARG* 2.5 37.9 + - - +
131I TYR* 3.5 22.2 + - - +
422I TYR 4.6 3.3 - - - +
423I LEU* 3.7 23.2 - - + +
426I TYR* 3.2 46.8 - - + +
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Residues in contact with ALA 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I ALA 3.2 13.4 + - - +
125I CYS* 3.5 10.8 - - - +
126I LYS 3.2 0.4 - - - -
127I GLU* 1.3 76.5 - - - +
129I VAL* 1.3 52.4 + - - +
131I TYR* 3.0 5.0 + - - +
132I ILE* 2.6 40.5 + - + +
419I LEU* 3.8 28.1 - - + +
423I LEU* 4.4 4.4 - - + +
441I PHE* 5.9 2.0 - - + -
514I LEU* 3.8 25.4 - - + -
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Residues in contact with VAL 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I CYS* 3.3 27.0 + - - +
126I LYS* 3.5 9.4 + - + +
127I GLU 3.4 0.4 - - - -
128I ALA* 1.3 75.1 - - + +
130I ARG* 1.3 53.1 + - + +
132I ILE* 3.4 10.4 - - + +
133I ASN* 2.7 50.3 + - - +
511I VAL* 4.3 29.2 - - + +
514I LEU* 5.0 2.5 - - + -
515I LYS* 5.4 3.8 - - - +
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Residues in contact with ARG 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123I LEU* 4.5 6.7 - - - +
126I LYS* 3.1 44.4 + - - +
127I GLU* 2.5 43.0 + - - +
128I ALA 3.2 0.8 - - - -
129I VAL* 1.3 78.7 - - + +
131I TYR* 1.3 60.5 + - - +
133I ASN* 3.2 20.8 + - - +
134I GLU* 3.2 22.5 + - - +
426I TYR* 3.5 18.2 + - - -
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Residues in contact with TYR 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I GLU* 3.5 14.6 + - - +
128I ALA 3.0 6.5 + - - +
130I ARG* 1.3 76.4 - - - +
132I ILE* 1.3 60.6 + - - +
133I ASN 3.2 0.2 - - - -
134I GLU* 2.9 41.4 + - + +
135I ASN* 3.0 40.5 + - - -
137I ILE* 4.8 1.9 - - - +
415I VAL* 5.7 0.9 - - + -
418I ALA* 4.1 22.9 - - + +
419I LEU* 4.3 19.1 - - + -
422I TYR* 5.9 4.9 - + + -
423I LEU* 6.1 1.1 - - + -
476I VAL 5.0 6.9 + - - -
478I PRO* 3.3 42.6 - - + +
484I LYS* 4.0 14.7 + - - -
486I ILE* 4.8 6.6 - - + +
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Residues in contact with ILE 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I ALA* 2.6 29.9 + - + +
129I VAL* 3.4 8.7 - - + +
131I TYR* 1.3 72.2 - - - +
133I ASN* 1.3 64.2 + - - +
134I GLU 3.3 0.7 + - - -
135I ASN* 3.4 18.0 + - - +
407I SER* 4.1 6.9 - - - -
408I VAL 4.7 0.3 - - - +
409I VAL* 3.5 31.0 - - + +
415I VAL* 4.9 8.1 - - + -
419I LEU* 5.0 7.6 - - + -
507I THR* 3.7 27.3 + - + -
510I LYS* 5.2 5.8 - - + -
511I VAL* 3.7 24.7 - - + +
514I LEU* 3.7 25.6 - - + -
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Residues in contact with ASN 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I VAL* 2.7 33.2 + - - +
130I ARG* 3.2 13.6 + - - +
132I ILE* 1.3 81.7 - - - +
134I GLU* 1.3 59.2 + - + +
135I ASN 3.3 2.1 + - - +
407I SER* 2.8 33.7 + - - +
507I THR* 4.7 7.3 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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