Contacts of the helix formed by residues 72 - 85 (chain B) in PDB entry 3ISL
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 THR 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASP* 3.7 15.3 - - + +
250A TYR* 3.0 33.2 + - - +
268A HIS* 3.8 11.2 - - - +
269A THR 3.2 25.1 - - - +
71B GLY* 1.3 77.8 - - - +
73B SER* 1.3 67.7 + - - +
74B ARG 3.1 0.9 + - - -
75B ALA 3.0 10.6 + - - -
76B GLY 3.3 6.9 + - - -
206B SER* 4.5 2.0 - - - -
207B GLY* 4.2 16.4 - - - +
208B MET 4.4 0.2 - - - +
209B ALA* 3.3 3.8 - - - +
419B PLP 2.7 29.6 + - - -
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B THR* 1.3 71.3 - - - +
74B ARG* 1.3 56.1 + - - +
76B GLY* 3.0 18.0 + - - -
77B ILE* 3.1 17.5 + - - +
176B VAL* 3.6 28.2 - - - +
195B ILE* 3.7 3.1 - - - +
196B GLY 4.2 3.8 - - - -
197B GLY* 3.6 11.1 - - - -
199B GLN* 3.7 7.8 + - - -
208B MET 4.2 3.0 + - - -
209B ALA* 3.8 11.5 - - - +
419B PLP 2.5 39.6 + - - -
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ASN* 4.5 8.0 - - - +
250A TYR* 4.0 14.6 - - + -
266A ASN* 3.5 22.0 + - - +
267A HIS* 3.1 29.4 + - - +
268A HIS* 3.5 13.6 - - - +
269A THR* 5.0 0.2 + - - -
72B THR 3.1 0.2 - - - -
73B SER* 1.3 72.9 - - - +
75B ALA* 1.3 61.3 + - - +
77B ILE* 3.4 11.8 + - - +
78B GLU* 2.9 29.8 + - - +
98B ARG* 3.2 28.1 - - - +
99B PHE* 4.1 10.6 - - - -
102B LEU* 3.7 38.9 - - + +
106B ILE* 4.4 3.2 - - + +
419B PLP 2.9 49.2 + - - +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A TYR* 3.7 28.5 - - + -
69B ILE* 3.9 3.8 - - + -
71B GLY* 3.8 10.8 - - - -
72B THR 3.0 10.8 + - - +
74B ARG* 1.3 77.1 - - - +
76B GLY* 1.3 55.1 + - - +
78B GLU* 3.7 2.4 - - - +
79B ALA* 2.8 35.2 + - - +
251B PHE* 3.3 35.0 - - + -
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Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 3.7 21.0 - - - +
72B THR 3.3 3.8 + - - -
73B SER 3.0 8.9 + - - -
75B ALA* 1.3 76.0 - - - +
77B ILE* 1.3 62.5 + - - +
79B ALA* 3.3 2.9 + - - +
80B VAL* 3.1 27.5 + - - +
195B ILE* 3.9 10.3 - - - -
209B ALA* 3.7 10.2 - - - +
211B ILE* 4.4 4.4 - - - +
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER 3.1 13.6 + - - +
74B ARG* 3.6 11.9 - - - +
76B GLY* 1.3 73.2 - - - +
78B GLU* 1.3 56.3 + - - +
80B VAL* 3.4 3.1 + - - +
81B LEU* 3.0 38.5 + - + +
102B LEU* 4.4 8.5 - - + -
103B LEU* 3.6 26.5 - - + -
106B ILE* 3.9 9.9 - - + -
172B ILE* 6.3 0.4 - - + -
174B ASP* 3.3 36.3 - - + +
176B VAL* 4.4 2.5 - - + -
195B ILE* 3.6 30.2 - - + +
419B PLP 4.0 14.8 - - + -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A SER* 2.9 28.1 + - - -
249A ASN* 3.4 11.3 + - - +
250A TYR* 3.1 26.0 + - - +
74B ARG 2.9 18.2 + - - +
75B ALA* 3.7 4.3 - - - +
77B ILE* 1.3 72.8 - - - +
79B ALA* 1.3 56.4 + - - +
81B LEU* 4.0 0.3 - - - +
82B ALA* 2.7 38.5 + - - +
106B ILE* 4.0 21.5 - - + +
110B TYR* 2.8 38.3 + - + +
251B PHE* 3.9 13.6 - - + -
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 4.6 8.1 - - + -
75B ALA 2.8 21.4 + - - +
76B GLY* 3.5 8.3 - - - +
78B GLU* 1.3 73.1 - - - +
80B VAL* 1.3 61.1 + - + +
82B ALA* 4.0 0.2 - - - +
83B SER* 3.2 24.4 + - - -
211B ILE* 5.8 0.2 - - + -
251B PHE* 3.4 41.9 - - + +
253B LEU* 3.8 17.5 - - + +
256B LEU* 5.3 0.2 - - + -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLY 3.1 14.8 + - - +
77B ILE 3.8 5.2 - - - +
79B ALA* 1.3 71.1 - - - +
81B LEU* 1.3 68.5 + - - +
83B SER* 2.8 19.7 + - - +
84B VAL* 3.2 11.1 + - + +
172B ILE* 3.8 33.7 - - + -
193B ALA* 3.9 19.7 - - + -
194B ALA 5.4 0.2 - - - +
195B ILE* 3.7 21.1 - - + -
211B ILE* 4.2 15.7 - - + -
212B THR 6.0 0.2 - - - +
213B TYR* 5.3 2.7 - - + -
217B VAL* 5.4 2.9 - - + -
253B LEU* 3.7 20.0 - - + -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 3.0 37.1 + - + +
78B GLU 4.0 2.0 - - - +
80B VAL* 1.3 76.3 - - - +
82B ALA* 1.3 57.0 + - - +
84B VAL* 3.3 3.0 + - + -
85B ILE* 2.8 56.4 + - + +
91B VAL* 5.2 1.8 - - + -
103B LEU* 4.1 20.4 - - + +
106B ILE* 3.8 29.6 - - + -
107B ALA* 4.9 1.8 - - + +
110B TYR* 5.4 0.9 - - - -
141B ILE* 4.6 10.5 - - + -
143B ALA* 4.3 21.3 - - + -
172B ILE* 4.4 19.5 - - + -
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 2.7 24.6 + - + +
79B ALA* 4.0 5.6 - - - +
81B LEU* 1.3 72.8 - - - +
83B SER* 1.3 57.3 + - - +
85B ILE 3.7 4.2 - - - +
110B TYR* 3.6 46.7 - - + +
224B ARG* 3.0 21.1 + - - -
246B ILE* 3.7 20.0 - - + +
247B THR 4.9 0.3 + - - -
248B SER* 5.2 0.2 - - - -
251B PHE* 4.8 4.0 - - + +
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Residues in contact with SER 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ALA 3.2 13.8 + - - -
80B VAL* 2.8 15.6 + - - +
82B ALA* 1.3 78.0 - - - +
84B VAL* 1.3 61.6 + - - +
220B VAL* 4.5 0.5 - - - +
221B ILE* 3.5 27.5 - - - +
224B ARG* 3.2 17.5 + - - -
246B ILE* 3.3 26.3 - - - +
253B LEU* 3.4 31.2 - - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B VAL* 3.5 12.6 - - + +
81B LEU* 3.8 7.2 - - + +
83B SER* 1.3 90.4 + - - +
85B ILE* 1.3 60.0 + - + +
89B ASP* 3.5 0.5 - - - +
140B LYS* 2.9 30.4 + - - -
141B ILE* 3.7 16.9 - - + +
170B LEU* 4.2 10.8 - - + -
172B ILE* 3.6 27.6 - - + -
217B VAL* 4.0 25.8 - - + -
220B VAL* 4.0 21.3 - - + -
221B ILE* 4.3 2.7 - - + -
224B ARG* 4.0 1.8 - - - -
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LEU* 2.8 44.0 + - + +
82B ALA 3.7 4.3 - - - +
84B VAL* 1.3 73.6 - - + +
86B GLU* 1.3 71.6 + - - +
87B PRO* 4.9 0.2 - - - +
89B ASP* 3.8 4.0 - - + +
91B VAL* 3.9 16.6 - - + -
106B ILE 5.3 0.2 - - - +
107B ALA* 3.8 29.6 - - + -
110B TYR* 3.7 30.3 - - + +
112B ALA* 3.7 18.8 - - + +
141B ILE* 3.7 20.0 - - + -
224B ARG* 2.7 26.9 + - - -
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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