Contacts of the strand formed by residues 36 - 44 (chain B) in PDB entry 1IR1
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 ILE 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B THR 4.0 5.4 - - - +
35B ASP* 1.3 72.8 - - - +
37B LEU* 1.3 66.6 + - - +
102B ALA* 3.6 0.9 - - - -
103B TYR* 2.8 44.0 + - + +
105B LEU* 4.3 11.2 - - + -
108B PHE* 3.6 36.1 - - + -
116B MET* 5.4 7.9 - - - -
120B ILE* 4.0 27.1 - - + -
138B LEU* 4.2 8.3 - - + -
139B ARG 3.4 10.3 - - - +
140B ILE* 5.0 2.7 - - + -
141B PRO* 3.6 27.8 - - + -
144B TYR* 4.7 12.6 - - + -
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Residues in contact with LEU 37 (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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31B THR* 3.8 32.1 - - + +
35B ASP* 3.9 11.4 - - + -
36B ILE* 1.3 76.7 - - - +
38B ALA* 1.3 60.3 - - - +
85B TYR* 3.7 17.3 - - - +
101B VAL 3.3 2.2 - - - -
102B ALA* 3.8 19.5 - - + -
138B LEU* 3.2 8.3 - - - +
139B ARG* 2.7 71.6 + - + +
364B PHE* 3.7 26.1 - - + -
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Residues in contact with ALA 38 (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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37B LEU* 1.3 75.3 - - - +
39B ALA* 1.3 60.3 + - - +
40B PHE* 3.8 26.5 - - + -
99B CYS 3.6 1.2 - - - +
100B TYR* 3.3 5.7 - - - -
101B VAL* 2.8 35.4 + - + +
103B TYR* 3.9 15.7 - - + -
120B ILE* 4.6 0.9 - - + -
135B LEU* 4.0 4.9 - - + -
137B ASP 3.5 4.0 - - - -
138B LEU* 3.7 18.2 - - + -
364B PHE* 3.8 5.0 - - - -
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Residues in contact with ALA 39 (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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38B ALA* 1.3 71.6 - - - +
40B PHE* 1.3 61.3 + - - +
98B ILE* 4.4 5.6 - - + -
99B CYS 3.8 2.9 - - - -
100B TYR* 4.1 8.3 - - + -
135B LEU* 3.7 2.4 - - - +
136B GLU* 2.9 29.4 + - + +
137B ASP 3.0 14.4 + - - +
363B TYR* 3.9 31.0 - - + -
364B PHE* 3.7 20.8 - - + -
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Residues in contact with PHE 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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38B ALA* 3.8 17.3 - - + -
39B ALA* 1.3 74.2 - - - +
41B ARG* 1.3 58.9 + - - +
42B VAL* 3.4 16.6 + - + -
57B VAL* 3.7 20.4 - - + -
97B TYR 3.4 1.2 - - - +
98B ILE* 3.2 7.5 - - - -
99B CYS* 2.8 42.5 + - + +
101B VAL* 3.8 21.1 - - + -
103B TYR* 3.7 18.6 - - - -
120B ILE* 3.6 36.8 - - + -
124B VAL* 4.9 0.4 - - + -
125B PHE* 4.3 11.9 - + - -
133B LEU* 3.8 20.0 - - + -
134B ARG 3.4 6.5 - - - -
135B LEU* 3.9 22.9 - - + -
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Residues in contact with ARG 41 (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 ALA 4.1 1.0 + - - -
40B PHE* 1.3 69.2 - - - +
42B VAL* 1.3 59.8 + - - +
43B SER* 4.1 1.5 + - - +
90B VAL* 3.9 18.2 - - - +
96B GLN* 3.1 43.9 + - + +
97B TYR 3.5 4.0 - - - +
98B ILE* 3.9 15.2 - - + +
133B LEU* 3.5 5.9 - - - +
134B ARG* 2.6 40.6 + - + +
136B GLU* 2.8 37.9 + - + +
305B LYS* 3.1 47.7 + - - +
306B ASN* 4.5 5.4 - - - +
363B TYR* 3.7 11.5 + - - -
474B THR 4.9 0.6 + - - -
475B VAL* 3.7 20.4 + - - +
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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 PHE* 3.8 14.8 - - + +
41B ARG* 1.3 75.7 - - - +
43B SER* 1.3 63.8 + - - +
44B PRO* 3.5 10.4 - - + +
53B ALA* 4.1 17.7 - - + +
54B GLY* 5.3 0.7 - - - -
57B VAL* 4.9 7.4 - - + -
96B GLN* 3.4 4.3 - - - -
97B TYR* 2.7 41.2 + - + +
99B CYS* 3.8 28.3 - - + -
130B LEU* 3.8 27.6 - - + -
132B ALA 4.8 0.2 - - - +
133B LEU* 3.7 20.4 - - + -
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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 ARG* 4.1 1.4 + - - +
42B VAL* 1.3 74.0 - - - +
44B PRO* 1.3 58.4 - - - +
94B GLU 5.7 0.4 + - - -
95B ASN 3.8 4.7 - - - -
96B GLN* 3.4 30.3 + - - +
130B LEU* 3.7 1.4 - - - -
131B ARG* 2.8 51.6 + - - +
132B ALA* 3.1 34.3 + - - +
306B ASN* 4.9 2.9 + - - +
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Residues in contact with PRO 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* 3.5 11.4 - - + +
43B SER* 1.3 87.0 - - - +
45B GLN* 1.3 61.5 + - - +
48B VAL* 3.6 27.1 - - + +
50B PRO* 4.7 3.8 - - + -
53B ALA* 4.0 26.0 - - + -
95B ASN* 3.1 41.6 + - - +
97B TYR* 4.2 17.5 - - + -
129B ALA 3.9 6.1 - - - +
130B LEU* 4.4 4.3 - - + -
131B ARG* 3.6 12.6 + - - -
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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