Contacts of the strand formed by residues 130 - 139 (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 LEU 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.9 13.9 - - + -
43A SER 3.8 4.0 - - - +
44A PRO* 4.4 3.6 - - + -
45A GLN* 3.6 12.3 + - - -
53A ALA* 3.9 32.1 - - + +
56A ALA* 6.1 2.9 - - + -
57A VAL* 4.1 13.0 - - + -
124A VAL* 3.6 23.8 - - + +
125A PHE* 5.4 3.1 - - - +
127A PHE* 3.1 27.0 + - + +
128A LYS 3.1 1.3 - - - +
129A ALA* 1.3 89.1 - - + +
131A ARG* 1.3 61.2 + - - +
132A ALA 4.3 7.9 - - - +
133A LEU* 4.1 25.1 - - + -
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Residues in contact with ARG 131 (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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43A SER* 2.7 24.3 + - - +
44A PRO 2.6 24.5 + - - +
45A GLN* 3.6 30.2 - - - +
46A PRO* 4.5 8.5 - - - -
94A GLU* 3.9 14.1 + - - +
95A ASN* 2.7 42.8 + - - +
130A LEU* 1.3 74.3 - - - +
132A ALA* 1.3 65.0 + - + +
307A HIS* 4.9 2.1 + - - -
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Residues in contact with ALA 132 (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* 4.2 0.9 - - - +
43A SER* 3.1 39.1 + - - +
125A PHE 6.0 0.4 - - - -
130A LEU* 3.5 7.2 - - - +
131A ARG* 1.3 84.3 - - + +
133A LEU* 1.3 64.3 + - - +
306A ASN* 3.3 37.5 - - + +
307A HIS* 3.7 13.2 - - + +
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Residues in contact with LEU 133 (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* 3.8 20.2 - - + -
41A ARG 3.5 9.4 - - - +
42A VAL* 3.6 32.3 - - + -
57A VAL* 4.4 9.6 - - + -
124A VAL* 3.7 44.2 - - + +
125A PHE* 3.1 38.2 - - + +
130A LEU* 4.1 13.5 - - + -
132A ALA* 1.3 77.9 - - - +
134A ARG* 1.3 62.5 + - - +
306A ASN 3.6 2.9 + - - -
307A HIS* 3.2 7.3 + - - -
308A GLY 3.0 19.2 + - - -
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Residues in contact with ARG 134 (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* 3.4 6.1 - - - -
41A ARG* 2.7 45.6 + - + +
125A PHE* 4.5 0.4 - - - -
133A LEU* 1.3 77.2 - - - +
135A LEU* 1.3 65.8 + - - +
136A GLU* 3.0 33.5 + - - -
302A ASP 3.1 24.4 + - - -
304A GLN 3.3 19.9 + - - -
305A LYS* 3.3 27.6 - - - +
306A ASN 4.0 10.5 - - - +
307A HIS* 4.0 0.6 + - - -
308A GLY 3.1 24.7 - - - +
309A MET 4.4 2.2 - - - +
310A HIS* 3.5 24.3 - - - +
473A ASP* 2.7 30.5 + - - -
474A THR 5.3 2.0 + - - -
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Residues in contact with LEU 135 (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* 4.0 8.1 - - + -
39A ALA 3.8 8.5 - - - +
40A PHE* 3.8 26.7 - - + -
117A PHE* 5.0 1.3 - - + -
120A ILE* 4.2 7.9 - - + -
121A VAL* 3.8 21.8 - - + -
125A PHE* 4.0 5.8 - - + -
134A ARG* 1.3 71.7 - - - +
136A GLU* 1.3 58.2 + - - +
137A ASP 3.6 19.5 - - - +
138A LEU* 4.0 16.6 - - + -
308A GLY 3.0 7.5 + - - -
309A MET* 3.5 16.5 - - + -
310A HIS* 3.0 25.5 + - - +
313A VAL* 3.8 34.1 - - + +
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Residues in contact with GLU 136 (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* 2.8 19.3 + - + +
41A ARG* 2.8 54.6 + - + +
98A ILE* 4.9 2.2 - - + -
134A ARG* 3.0 31.7 + - - +
135A LEU* 1.3 74.8 - - - +
137A ASP* 1.3 57.8 + - - +
310A HIS* 3.8 4.3 - - - +
312A ARG* 2.7 55.2 + - - +
313A VAL* 3.7 3.4 - - - +
363A TYR* 3.8 29.5 - - + +
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Residues in contact with ASP 137 (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* 3.1 23.8 + - + -
135A LEU* 3.6 4.6 - - - +
136A GLU* 1.3 79.8 - - - +
138A LEU* 1.3 83.6 + - - +
312A ARG* 3.9 15.1 - - - +
313A VAL* 3.8 9.2 - - - +
316A LYS* 3.0 29.1 + - - +
348A LEU* 5.4 0.7 - - - +
362A ILE* 4.0 8.5 - - - +
363A TYR* 3.1 44.8 + - + -
364A PHE* 3.5 17.7 + - + +
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Residues in contact with LEU 138 (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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36A ILE* 4.4 3.6 - - + -
37A LEU 3.2 6.7 - - - +
38A ALA* 3.4 31.2 - - + -
116A MET* 4.1 24.9 - - + -
117A PHE* 4.4 3.4 - - + -
120A ILE* 3.9 25.1 - - + -
135A LEU* 4.0 13.2 - - + -
137A ASP* 1.3 86.4 + - - +
139A ARG* 1.3 57.2 + - - +
140A ILE* 3.6 15.2 + - + -
313A VAL* 3.9 26.2 - - + +
316A LYS* 2.7 37.8 + - + +
364A PHE* 3.9 3.4 - - - -
366A GLN* 3.4 2.4 - - - +
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Residues in contact with ARG 139 (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* 5.0 2.0 + - - -
32A LEU 3.0 24.9 + - - -
33A ASP* 4.1 18.0 + - - +
35A ASP 2.9 28.9 + - - +
36A ILE* 3.4 2.8 - - - +
37A LEU* 2.7 68.8 + - + +
138A LEU* 1.3 71.8 - - - +
140A ILE* 1.3 70.8 + - - +
141A PRO* 3.4 11.0 - - - +
364A PHE* 3.7 19.8 - - + -
365A THR 3.5 24.3 + - - +
366A GLN* 3.7 5.4 - - - +
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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