Contacts of the strand formed by residues 36 - 44 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A THR 3.9 5.2 - - - +
35A ASP* 1.3 72.3 - - - +
37A LEU* 1.3 66.8 + - - +
102A ALA* 3.5 0.7 - - - -
103A TYR* 2.8 44.0 + - + +
105A LEU* 4.3 10.8 - - + -
108A PHE* 3.6 36.3 - - + -
116A MET* 5.4 2.7 - - - -
120A ILE* 3.9 28.0 - - + -
138A LEU* 4.4 8.1 - - + -
139A ARG 3.4 8.5 - - - +
140A ILE* 4.9 5.6 - - + -
141A PRO* 3.5 29.4 - - + -
144A TYR* 4.7 13.7 - - + -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 3.6 33.7 - - + +
35A ASP* 3.8 11.4 - - + -
36A ILE* 1.3 75.7 - - - +
38A ALA* 1.3 60.1 + - - +
85A TYR* 3.8 16.2 - - - +
101A VAL 3.4 2.2 - - - -
102A ALA* 3.7 20.0 - - + -
138A LEU* 3.2 9.6 - - - +
139A ARG* 2.7 78.2 + - + +
364A PHE* 3.8 20.9 - - + -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 1.3 76.0 - - - +
39A ALA* 1.3 61.1 + - - +
40A PHE* 3.8 25.8 - - + -
99A CYS 3.6 1.2 - - - +
100A TYR* 3.4 5.2 - - - -
101A VAL* 2.8 32.1 + - - +
103A TYR* 3.9 16.6 - - + -
120A ILE* 4.5 0.4 - - + -
135A LEU* 4.0 3.8 - - + -
137A ASP 3.6 4.3 - - - -
138A LEU* 3.4 19.5 - - + -
364A PHE* 3.8 4.9 - - - -
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 1.3 72.9 - - - +
40A PHE* 1.3 62.0 + - - +
98A ILE* 4.4 4.9 - - + -
99A CYS 3.8 4.0 - - - -
100A TYR* 4.3 8.5 - - + -
135A LEU* 3.8 2.4 - - - +
136A GLU* 2.8 30.9 + - + +
137A ASP 3.1 12.6 + - - +
363A TYR* 3.9 29.8 - - + -
364A PHE* 3.7 19.7 - - + -
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Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 3.8 17.3 - - + -
39A ALA* 1.3 73.0 - - - +
41A ARG* 1.3 60.0 + - - +
42A VAL* 3.5 17.3 + - + -
57A VAL* 3.7 24.0 - - + -
97A TYR 3.5 0.7 - - - +
98A ILE* 3.2 7.8 - - - -
99A CYS* 2.8 41.1 + - + +
101A VAL* 4.0 18.4 - - + -
103A TYR* 3.6 18.2 - - - -
120A ILE* 3.7 37.0 - - + -
124A VAL* 4.8 0.4 - - + -
125A PHE* 4.4 11.9 - + - -
133A LEU* 3.8 20.0 - - + -
134A ARG 3.4 6.1 - - - -
135A LEU* 3.8 22.7 - - + -
136A GLU* 5.1 0.2 - - - -
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Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA 4.2 0.4 + - - -
40A PHE* 1.3 69.4 - - - +
42A VAL* 1.3 59.5 + - - +
43A SER* 4.0 0.9 + - - -
90A VAL* 3.6 19.2 - - - +
96A GLN* 2.9 47.3 + - + +
97A TYR 3.4 3.8 - - - -
98A ILE* 4.0 14.5 - - + +
132A ALA 4.1 0.5 - - - +
133A LEU* 3.5 6.6 - - - -
134A ARG* 2.7 39.9 + - + +
136A GLU* 2.8 34.0 + - + +
305A LYS* 3.1 50.7 + - - +
306A ASN* 4.5 5.6 - - - +
363A TYR* 3.7 17.2 + - - -
474A THR 5.0 3.2 + - - -
475A VAL* 6.0 2.4 - - - +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.9 13.7 - - + +
41A ARG* 1.3 72.3 - - - +
43A SER* 1.3 64.8 + - - +
44A PRO* 3.4 11.6 - - + +
50A PRO* 6.4 0.2 - - + -
53A ALA* 4.0 17.9 - - + -
54A GLY* 5.3 0.2 - - - -
57A VAL* 4.8 7.9 - - + -
96A GLN* 3.4 4.1 - - - -
97A TYR* 2.7 40.5 + - + +
99A CYS* 3.7 29.4 - - + -
130A LEU* 3.9 26.5 - - + -
132A ALA 4.2 1.8 - - - -
133A LEU* 3.6 22.2 - - + -
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ARG 4.0 1.4 + - - -
42A VAL* 1.3 74.3 - - - +
44A PRO* 1.3 60.4 - - - +
95A ASN 3.7 0.9 - - - -
96A GLN* 3.4 26.7 + - - +
130A LEU* 3.7 1.3 - - - -
131A ARG* 2.7 53.8 + - - +
132A ALA* 3.1 35.5 + - - +
306A ASN* 4.8 3.5 + - - +
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Residues in contact with PRO 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.4 12.6 - - + +
43A SER* 1.3 85.9 - - - +
45A GLN* 1.3 58.5 + - - +
48A VAL* 3.6 26.7 - - + +
50A PRO* 4.6 4.0 - - + -
53A ALA* 3.9 26.2 - - + -
95A ASN* 3.1 36.4 + - - +
97A TYR* 4.3 16.6 - - + -
129A ALA 3.9 6.1 - - - +
130A LEU* 4.4 3.6 - - + -
131A ARG* 2.6 27.5 + - - -
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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
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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