Contacts of the strand formed by residues 39 - 44 (chain B) in PDB entry 4IRX
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 GLU 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B PRO 4.4 1.8 - - - +
34B ARG* 3.5 37.2 + - - +
35B GLY* 2.8 31.2 + - - -
36B SER* 3.6 15.3 + - - +
37B HIS 2.9 6.0 + - - +
38B MSE 1.3 79.5 - - - +
40B VAL* 1.3 68.9 + - - +
41B VAL* 6.1 0.4 - - + -
68B VAL* 3.6 1.4 - - - +
69B LYS* 3.2 35.5 + - + +
71B GLN* 3.2 29.3 + - + +
95B LYS 5.3 0.3 + - - -
96B VAL 4.8 4.2 + - - +
295B ILE* 3.7 9.0 - - - +
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Residues in contact with VAL 40 (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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39B GLU* 1.3 80.8 - - - +
41B VAL* 1.3 77.9 + - - +
42B VAL* 4.1 4.0 - - + -
68B VAL* 3.9 12.6 - - + -
69B LYS 2.9 7.5 + - - +
70B VAL* 3.3 7.6 - - + +
71B GLN* 3.0 23.6 + - - +
94B ALA* 6.3 0.7 - - - -
96B VAL* 3.7 15.3 - - + +
98B ILE* 3.9 29.2 - - + -
288B LEU* 4.2 11.2 - - + -
291B ALA* 3.9 18.4 - - + -
292B VAL* 5.2 0.4 - - + -
295B ILE* 3.7 20.2 - - + -
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 5.2 6.3 - - + -
34B ARG* 6.1 1.1 - - + +
39B GLU* 6.5 0.4 - - + -
40B VAL* 1.3 78.4 - - - +
42B VAL* 1.3 62.6 + - - +
43B SER* 4.7 1.3 - - - +
71B GLN* 3.4 23.8 - - + +
73B LEU* 3.7 29.4 - - + -
86B LEU* 5.3 1.1 - - + -
89B ALA* 4.0 15.9 - - + -
94B ALA* 3.9 22.2 - - + +
96B VAL 3.5 4.8 + - - -
97B VAL* 3.3 23.5 - - + +
98B ILE 2.9 24.3 + - - -
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Residues in contact with VAL 42 (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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40B VAL* 4.1 13.9 - - + -
41B VAL* 1.3 79.5 - - - +
43B SER* 1.3 63.0 + - - +
44B PHE* 3.6 30.4 + - + -
59B LEU* 3.9 31.9 - - + -
70B VAL* 4.4 11.4 - - + -
71B GLN 2.9 9.9 + - - +
72B VAL* 3.4 4.4 - - + -
73B LEU 2.9 26.7 + - - +
98B ILE* 3.2 28.5 - - + +
100B ALA 6.2 0.2 - - - +
124B VAL* 5.7 1.8 - - + -
284B ILE* 4.5 5.8 - - + -
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Residues in contact with SER 43 (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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41B VAL* 4.1 1.0 - - - -
42B VAL* 1.3 71.2 - - - +
44B PHE* 1.3 62.4 + - - +
73B LEU* 3.6 17.7 + - - +
75B ALA* 4.9 1.2 - - - +
82B GLN* 2.9 32.9 + - - +
85B ASP* 5.0 2.3 + - - +
86B LEU* 3.8 26.4 - - - +
97B VAL* 4.8 0.9 - - - -
98B ILE 2.8 12.9 + - - +
99B VAL* 3.5 4.6 - - - -
100B ALA* 2.9 27.9 + - - +
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Residues in contact with PHE 44 (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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42B VAL* 3.6 28.5 - - + -
43B SER* 1.3 73.5 + - - +
45B ASN* 1.3 60.3 + - - +
46B ASP 4.3 3.4 - - - +
47B LEU* 3.7 27.6 - - + +
52B PHE* 3.8 39.7 - + + -
55B MSE 4.0 17.7 - - + -
56B ARG* 4.1 25.1 - - + -
59B LEU* 4.1 11.4 - - + -
72B VAL* 3.7 31.6 - - + -
73B LEU 2.8 11.6 + - - +
74B ASP* 4.7 0.7 - - - -
75B ALA* 2.8 30.1 + - - +
82B GLN* 3.9 1.1 - - - -
100B ALA* 3.9 6.5 - - + -
124B VAL* 5.8 1.8 - - + -
284B ILE* 5.1 2.5 - - + -
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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
------------------------------------------------------------
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