Contacts of the strand formed by residues 33 - 44 (chain B) in PDB entry 1I3R
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 PHE 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.5 5.6 - - - -
15A LEU* 3.0 44.8 + - + +
16A PRO* 5.1 3.8 - - + -
70A LEU* 3.8 21.9 - - + +
74A LYS* 3.5 37.2 - - + -
79A ASN* 3.8 32.3 - - + -
80A THR 3.9 13.9 - - - -
81A PRO* 4.3 3.4 - - + -
31B PRO* 4.5 18.2 - - + -
32B TRP* 1.3 93.9 - - - +
34B LEU* 1.3 59.9 + - - +
58B TYR* 3.3 20.2 - + - +
59B ASN* 3.2 4.9 - - - +
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Residues in contact with LEU 34 (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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12A PHE* 3.7 39.0 - - + -
13A TYR 3.8 6.1 - - - +
14A LEU* 4.0 5.8 - - + -
70A LEU* 4.1 4.0 - - - +
113A SER* 4.1 10.3 - - - +
115A PRO* 3.9 16.6 - - + -
143A HIS 5.3 0.4 - - - +
145A PHE* 3.7 25.6 - - + -
32B TRP* 3.7 15.3 - - + -
33B PHE* 1.3 74.3 - - - +
35B GLU* 1.3 58.3 + - - +
36B TYR* 3.9 17.9 - - + -
57B PHE 3.6 0.5 - - - +
58B TYR* 3.2 11.1 - - - -
59B ASN* 2.8 51.5 + - - +
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Residues in contact with GLU 35 (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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11A GLN 4.0 0.2 - - - +
12A PHE* 3.0 26.3 - - - +
13A TYR 3.2 10.3 + - - +
66A ASN* 3.6 40.2 + - + +
69A ASN* 3.7 15.5 + - + +
70A LEU* 3.9 16.2 - - + +
73A MET* 3.3 22.9 - - - +
13B LYS* 2.7 32.6 + - - -
34B LEU* 1.3 71.6 - - - +
36B TYR* 1.3 61.7 + - - +
37B CYS* 4.4 0.7 + - - +
56B TYR* 4.5 8.5 - - - -
57B PHE 3.8 8.7 - - - +
58B TYR* 4.3 3.1 - - - +
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Residues in contact with TYR 36 (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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10A ALA* 4.3 4.5 - - + +
11A GLN 3.2 24.2 - - - -
12A PHE* 3.6 12.1 - + + -
138A LEU 5.0 0.2 - - - -
139A PRO* 3.5 18.7 - - - +
143A HIS 4.0 19.7 - - - -
144A LEU 4.7 1.5 + - - -
145A PHE* 3.3 41.2 - + - -
34B LEU* 3.9 16.4 - - + -
35B GLU* 1.3 76.4 - - - +
37B CYS* 1.3 63.5 + - - +
38B LYS* 3.3 41.9 - - + +
56B TYR* 3.5 2.1 - - - +
57B PHE* 2.6 68.1 + + + +
59B ASN 5.8 0.2 - - - -
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Residues in contact with CYS 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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9A GLN 3.7 1.6 - - - +
10A ALA* 3.6 2.1 - - - -
11A GLN* 3.0 41.2 + - + +
66A ASN* 4.7 6.1 - - - +
10B GLU* 2.8 38.1 - - - +
35B GLU* 4.3 1.5 - - + +
36B TYR* 1.3 76.8 - - - +
38B LYS* 1.3 67.3 + - - +
39B SER* 4.2 6.5 - - - -
54B VAL* 3.8 22.4 - - - -
55B ARG 3.3 6.3 - - - +
56B TYR* 3.8 15.9 - - + -
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Residues in contact with LYS 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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8A ILE* 4.2 12.2 - - + +
9A GLN 3.4 3.8 - - - -
10A ALA* 4.0 8.1 - - + -
139A PRO* 3.7 14.6 - - + -
140A ARG 2.5 30.5 + - - +
141A ASP* 3.7 6.9 + - - +
142A ASP 2.8 23.9 + - - -
144A LEU 5.5 0.2 + - - -
36B TYR* 3.3 34.9 + - + +
37B CYS* 1.3 78.9 - - - +
39B SER* 1.3 60.2 + - - +
40B GLU* 3.7 10.3 + - + +
53B LEU 3.6 4.0 - - - +
54B VAL* 3.4 1.4 - - - -
55B ARG* 2.7 50.7 + - + +
57B PHE* 3.8 18.6 - - + -
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Residues in contact with SER 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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7A ILE 3.8 1.4 - - - +
8A ILE* 3.4 2.2 - - - -
9A GLN* 3.0 35.3 + - - -
8B PHE* 3.5 46.6 - - - +
10B GLU* 5.0 2.6 + - - -
37B CYS* 4.2 7.3 - - - -
38B LYS* 1.3 70.4 - - - +
40B GLU* 1.3 61.1 + - - +
52B LEU* 4.6 1.1 - - - -
53B LEU 4.1 2.7 - - - -
54B VAL* 3.5 30.2 - - - +
97B LYS* 5.4 0.9 + - - -
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Residues in contact with GLU 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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6A THR* 4.6 0.4 - - + -
7A ILE 3.5 4.0 - - - -
8A ILE* 3.8 32.3 - - + +
140A ARG 5.4 0.3 - - - +
141A ASP* 5.6 1.4 - - - -
38B LYS* 4.2 14.9 + - + +
39B SER* 1.3 73.9 - - - +
41B CYS* 1.3 61.4 + - - +
42B HIS* 2.9 33.2 + - + +
51B ARG 3.6 1.9 - - - +
52B LEU* 3.5 4.4 - - - +
53B LEU* 2.9 55.9 + - - +
55B ARG* 2.8 35.2 + - - -
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Residues in contact with CYS 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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6A THR* 3.4 7.6 - - - +
7A ILE* 2.8 41.7 + - + +
8B PHE* 3.4 23.3 - - - -
40B GLU* 1.3 73.2 - - - +
42B HIS* 1.3 60.7 + - - +
43B PHE* 3.5 22.1 - - + -
50B VAL* 4.9 0.2 - - + -
51B ARG 3.6 4.9 - - - +
104B VAL* 5.1 0.7 - - - -
105B CYS* 2.0 51.8 - - + -
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Residues in contact with HIS 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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5A HIS 3.9 2.5 - - - -
6A THR* 3.9 25.9 + - + -
40B GLU* 2.9 44.5 + - + +
41B CYS* 1.3 72.4 - - - +
43B PHE* 1.3 62.7 + - - +
44B TYR* 3.8 30.4 + - + +
49B ARG 3.7 1.4 - - - +
50B VAL* 3.4 6.1 - - - +
51B ARG* 2.7 56.4 + - + +
53B LEU* 4.1 15.3 - - + +
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Residues in contact with PHE 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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3A GLU 4.3 2.0 - - - +
4A GLU* 3.4 4.3 - - - +
5A HIS* 2.9 47.4 + - + +
7A ILE* 3.6 20.6 - - + -
41B CYS* 3.5 30.5 - - + -
42B HIS* 1.3 71.4 - - - +
44B TYR* 1.3 73.4 + - - +
45B ASN 4.2 0.4 - - - -
46B GLY 3.6 17.9 - - - +
47B THR* 4.2 3.6 - - + -
49B ARG 3.8 1.6 - - - -
50B VAL* 3.9 25.1 - - + -
105B CYS* 3.4 28.7 - - + -
109B TYR* 3.4 41.3 - + + -
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Residues in contact with TYR 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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3A GLU 4.1 0.4 - - - -
4A GLU* 4.1 26.0 - - + +
42B HIS* 3.8 36.9 + - + +
43B PHE* 1.3 79.4 - - - +
45B ASN* 1.3 75.1 + - - +
46B GLY 3.3 4.0 + - - +
48B GLN* 3.5 0.9 - - - +
49B ARG* 3.1 71.8 + - + +
51B ARG* 4.6 11.3 + - + -
304B NAG 3.6 20.8 - - + +
67D ASP* 5.0 3.1 + - - -
69D ASP 5.6 0.2 - - - -
70D VAL* 3.8 31.5 - - + +
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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