Contacts of the strand formed by residues 36 - 44 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D THR 3.8 1.3 + - - +
35D ASP* 1.3 73.2 - - - +
37D LEU* 1.3 68.0 + - - +
102D ALA* 3.5 1.9 - - - -
103D TYR* 2.8 41.5 + - + +
105D LEU* 5.6 2.0 - - + -
108D PHE* 3.4 42.0 - - + -
116D MET* 4.4 9.9 - - - -
120D ILE* 4.1 22.7 - - + -
138D LEU* 4.4 7.6 - - + -
139D ARG 3.4 11.2 - - - +
140D ILE* 5.2 2.7 - - + -
141D PRO* 3.5 20.0 - - + -
144D TYR* 3.9 26.2 - - + -
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D THR* 3.7 32.3 - - + +
35D ASP* 3.8 12.1 - - + -
36D ILE* 1.3 80.7 - - - +
38D ALA* 1.3 60.0 + - - +
85D TYR* 3.9 16.4 - - - +
101D VAL 3.4 2.5 - - - +
102D ALA* 3.8 13.9 - - + -
138D LEU* 3.1 9.3 - - - +
139D ARG* 2.7 77.5 + - + +
364D PHE* 3.8 21.2 - - + -
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Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 1.3 75.3 - - - +
39D ALA* 1.3 60.7 + - - +
40D PHE* 3.7 26.5 - - + -
99D CYS 3.6 1.2 - - - +
100D TYR* 3.3 5.7 - - - +
101D VAL* 2.8 34.9 + - - +
103D TYR* 3.9 16.4 - - + -
120D ILE* 4.5 0.7 - - + -
135D LEU* 4.0 3.1 - - + -
137D ASP 3.6 4.7 - - - -
138D LEU* 3.6 19.1 - - + -
364D PHE* 3.8 5.2 - - - -
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Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ALA* 1.3 72.8 - - - +
40D PHE* 1.3 61.1 + - - +
98D ILE* 4.3 5.6 - - + -
99D CYS 3.7 4.0 - - - -
100D TYR* 4.2 9.0 - - + -
135D LEU* 3.7 2.5 - - - +
136D GLU* 2.9 29.0 + - + +
137D ASP 3.1 13.5 + - - +
363D TYR* 3.9 30.5 - - + -
364D PHE* 3.8 21.3 - - + -
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Residues in contact with PHE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ALA* 3.7 16.8 - - + -
39D ALA* 1.3 76.4 - - - +
41D ARG* 1.3 61.2 + - - +
42D VAL* 3.4 18.7 + - + +
57D VAL* 3.8 23.6 - - + -
98D ILE* 3.2 7.1 - - - -
99D CYS* 2.9 35.7 + - + +
101D VAL* 4.0 17.5 - - + -
103D TYR* 3.7 17.7 - - - -
120D ILE* 3.6 37.5 - - + -
124D VAL* 4.7 0.2 - - + -
125D PHE* 4.3 16.2 - + - -
133D LEU* 3.8 22.4 - - + -
134D ARG 3.3 9.0 - - - -
135D LEU* 4.0 15.0 - - + -
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Residues in contact with ARG 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ALA 4.2 0.6 + - - -
40D PHE* 1.3 69.0 - - - +
42D VAL* 1.3 60.1 + - - +
43D SER* 4.1 1.3 + - - +
90D VAL* 3.8 19.8 - - + +
96D GLN* 3.1 44.6 + - + +
97D TYR 3.4 3.8 - - - +
98D ILE* 3.9 16.1 - - + +
132D ALA 4.2 0.5 - - - +
133D LEU* 3.5 5.4 - - - -
134D ARG* 2.7 41.0 + - + +
136D GLU* 2.9 39.8 + - + +
305D LYS* 3.1 57.3 + - - +
306D ASN* 4.5 5.4 - - - +
363D TYR* 3.7 13.1 + - - -
475D VAL 4.0 5.5 + - - -
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Residues in contact with VAL 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D PHE* 3.7 15.3 - - + +
41D ARG* 1.3 73.9 - - - +
43D SER* 1.3 64.4 + - - +
44D PRO* 3.5 9.1 - - + +
53D ALA* 4.1 18.4 - - + +
54D GLY* 5.3 0.2 - - - -
57D VAL* 4.9 6.7 - - + -
96D GLN* 3.3 5.4 - - - -
97D TYR* 2.7 41.9 + - + +
99D CYS* 3.7 29.2 - - + -
130D LEU* 3.8 26.0 - - + -
132D ALA 4.8 0.2 - - - +
133D LEU* 3.7 21.8 - - + -
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Residues in contact with SER 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ARG* 4.1 1.6 + - - +
42D VAL* 1.3 73.1 - - - +
44D PRO* 1.3 64.8 - - - +
95D ASN 3.7 7.6 + - - -
96D GLN* 3.3 30.7 + - - +
130D LEU* 3.7 1.8 - - - -
131D ARG* 2.8 43.7 + - - +
132D ALA* 3.1 34.2 + - - +
306D ASN* 4.9 2.9 + - - +
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Residues in contact with PRO 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D VAL* 3.5 12.3 - - + +
43D SER* 1.3 89.1 - - - +
45D GLN* 1.3 64.8 + - - +
48D VAL* 3.5 26.2 - - + +
50D PRO* 4.6 5.8 - - + -
53D ALA* 3.8 26.2 - - + -
95D ASN* 3.2 40.0 - - - +
97D TYR* 4.3 10.3 - - + -
129D ALA 3.9 5.6 - - - +
130D LEU* 4.3 4.0 - - + -
131D ARG* 3.7 14.3 + - - -
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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