Contacts of the strand formed by residues 33 - 44 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C LEU* 3.3 5.0 - - - +
15C LEU* 2.8 50.5 + - + -
16C PRO* 4.8 4.0 - - + -
70C LEU* 3.6 12.0 - - + +
74C LYS* 3.6 49.4 - - + -
79C ASN* 3.9 33.0 - - + -
81C PRO* 4.3 9.6 - - + -
31D PRO* 4.3 22.0 - - + -
32D TRP* 1.3 89.9 - - - +
34D LEU* 1.3 60.9 + - - +
58D TYR* 3.3 19.3 - - - +
59D ASN* 3.2 6.1 - - - +
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Residues in contact with LEU 34 (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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12C PHE* 3.7 34.1 - - + -
13C TYR 3.6 13.9 - - - +
14C LEU* 4.1 6.1 - - + -
70C LEU* 3.9 4.8 - - - +
113C SER* 4.0 7.2 - - - +
115C PRO* 3.9 17.3 - - + -
143C HIS 5.4 0.7 - - - +
145C PHE* 3.8 28.0 - - + -
32D TRP* 3.8 16.6 - - + -
33D PHE* 1.3 75.1 - - - +
35D GLU* 1.3 58.7 + - - +
36D TYR* 4.0 13.2 - - + -
57D PHE 3.6 0.9 - - - +
58D TYR* 3.4 9.0 - - - -
59D ASN* 2.7 52.4 + - - +
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Residues in contact with GLU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLN 4.0 0.3 - - - +
12C PHE* 3.1 5.5 - - - -
13C TYR 3.1 29.8 + - - +
66C ASN* 3.5 44.0 + - + +
69C ASN* 3.7 13.2 + - + +
70C LEU* 3.7 15.8 - - + +
73C MET* 3.2 22.4 - - - +
13D LYS* 2.7 32.7 + - - -
34D LEU* 1.3 71.8 - - - +
36D TYR* 1.3 62.7 + - - +
37D CYS* 5.9 1.1 - - + +
56D TYR* 4.6 8.7 - - - -
57D PHE 3.9 8.0 - - - +
58D TYR* 4.4 1.9 - - - -
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Residues in contact with TYR 36 (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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10C ALA* 4.2 9.2 - - + +
11C GLN 3.3 17.0 - - - -
12C PHE* 3.5 13.9 - + + -
138C LEU 5.0 0.2 - - - -
139C PRO* 3.6 19.1 - - - +
142C ASP 4.7 0.2 - - - -
143C HIS 4.4 16.8 - - - -
144C LEU 4.9 1.6 + - - -
145C PHE* 3.4 37.1 - + - -
34D LEU* 4.0 17.5 - - + -
35D GLU* 1.3 77.5 - - - +
37D CYS* 1.3 65.0 + - - +
38D LYS* 3.2 46.3 + - + +
56D TYR* 3.7 1.9 - - - -
57D PHE* 2.8 66.0 + + + +
59D ASN 5.9 0.2 - - - -
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Residues in contact with CYS 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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9C GLN 3.7 1.4 - - - +
10C ALA* 3.4 2.4 - - - -
11C GLN* 2.8 47.6 + - + +
66C ASN* 4.6 6.7 - - - +
10D GLU* 2.8 37.2 - - - +
35D GLU* 4.3 1.3 - - - +
36D TYR* 1.3 77.0 - - - +
38D LYS* 1.3 67.1 + - - +
39D SER* 4.4 5.8 - - - -
54D VAL* 3.9 12.8 - - - -
55D ARG 3.5 8.7 - - - -
56D TYR* 3.6 19.5 - - + -
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Residues in contact with LYS 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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8C ILE* 4.2 11.6 - - + +
9C GLN 3.3 2.9 - - - -
10C ALA* 3.9 8.7 - - + -
139C PRO* 3.8 13.9 - - + -
140C ARG 2.7 24.2 + - - +
141C ASP 3.9 6.3 + - - -
142C ASP 2.6 31.1 + - - -
36D TYR* 3.2 31.5 + - + +
37D CYS* 1.3 79.5 - - - +
39D SER* 1.3 60.7 + - - +
40D GLU* 4.0 9.6 + - + +
53D LEU 3.8 1.7 - - - +
54D VAL* 3.3 1.6 - - - -
55D ARG* 2.7 50.8 + - + +
57D PHE* 3.5 21.3 - - + -
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Residues in contact with SER 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE 3.7 1.0 - - - +
8C ILE* 3.3 3.2 - - - -
9C GLN* 2.9 37.7 + - - +
8D PHE* 3.5 45.2 - - - +
10D GLU* 5.1 2.8 + - - -
37D CYS* 4.4 5.9 - - - -
38D LYS* 1.3 73.0 - - - +
40D GLU* 1.3 62.3 + - - +
53D LEU 3.8 2.9 - - - -
54D VAL* 3.7 26.6 - - - +
97D LYS* 5.5 0.5 + - - -
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Residues in contact with GLU 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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6C THR* 4.5 0.4 - - + -
7C ILE 3.4 3.6 - - - -
8C ILE* 3.9 30.1 - - + +
140C ARG 5.4 1.0 - - - +
141C ASP* 5.7 1.0 - - - -
38D LYS* 4.4 13.7 + - + +
39D SER* 1.3 77.6 - - - +
41D CYS* 1.3 59.7 + - - +
42D HIS* 3.1 34.2 + - + +
51D ARG 3.4 1.7 - - - +
52D LEU* 3.4 8.4 - - - +
53D LEU* 2.8 56.3 + - - +
55D ARG* 3.0 34.4 + - - -
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Residues in contact with CYS 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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6C THR* 3.4 4.6 - - - -
7C ILE* 2.7 41.8 + - + +
8D PHE* 3.3 27.4 - - - -
40D GLU* 1.3 72.0 - - - +
42D HIS* 1.3 60.4 + - - +
43D PHE* 3.4 26.4 - - + -
50D VAL* 4.9 0.4 - - + -
51D ARG 3.5 5.4 - - - -
52D LEU* 4.1 0.2 - - - -
104D VAL* 5.0 0.2 - - - -
105D CYS* 2.0 50.7 - - - -
108D ASN* 6.1 0.2 - - - -
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Residues in contact with HIS 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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5C HIS 3.7 3.8 - - - -
6C THR* 3.8 22.0 + - + -
40D GLU* 3.1 43.7 + - + +
41D CYS* 1.3 72.8 - - - +
43D PHE* 1.3 60.0 - - - +
44D TYR* 3.9 27.9 + - + +
49D ARG 4.0 0.2 - - - +
50D VAL* 3.4 6.4 - - - +
51D ARG* 2.8 60.6 + - + +
53D LEU* 4.3 15.3 - - + +
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Residues in contact with PHE 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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3C GLU 4.1 2.2 - - - +
4C GLU* 3.1 23.7 - - - +
5C HIS* 2.8 33.9 + - + +
7C ILE* 3.6 22.0 - - + -
41D CYS* 3.4 34.1 - - + -
42D HIS* 1.3 72.0 - - - +
44D TYR* 1.3 71.4 + - - +
45D ASN 4.0 0.4 - - - -
46D GLY 3.4 15.3 - - - +
47D THR* 4.8 0.7 - - + -
49D ARG 3.8 1.3 - - - -
50D VAL* 3.2 37.5 - - + -
105D CYS* 3.5 25.6 - - - -
106D ARG* 4.2 1.8 - - - -
109D TYR* 3.7 39.7 - + + -
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Residues in contact with TYR 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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67B ASP* 4.9 4.3 + - - -
69B ASP 5.5 0.4 - - - -
70B VAL* 3.5 31.5 - - + +
3C GLU 4.0 0.7 - - - -
4C GLU* 3.6 32.1 - - + +
42D HIS* 3.9 34.4 + - + +
43D PHE* 1.3 79.4 - - - +
45D ASN* 1.3 72.7 + - - +
46D GLY 3.8 0.6 + - - -
48D GLN* 3.7 2.1 - - - +
49D ARG* 2.8 78.4 + - + +
50D VAL* 5.3 0.2 - - - -
51D ARG* 4.9 11.5 + - + -
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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