Contacts of the strand formed by residues 33 - 44 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14G LEU* 3.5 4.7 - - - -
15G LEU* 2.9 47.8 + - + +
16G PRO* 5.1 2.5 - - + -
70G LEU* 3.7 9.9 - - + +
74G LYS* 3.6 50.9 - - + -
79G ASN* 3.8 30.1 - - + -
80G THR 3.9 13.0 - - - -
81G PRO* 4.4 2.9 - - + -
31H PRO* 4.2 19.5 - - + -
32H TRP* 1.3 90.8 - - - +
34H LEU* 1.3 62.0 + - - +
58H TYR* 3.3 19.5 - - - +
59H ASN* 3.2 7.4 - - - +
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Residues in contact with LEU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G PHE* 3.8 30.5 - - + -
13G TYR 3.6 14.4 - - - +
14G LEU* 3.9 11.0 - - + -
70G LEU* 4.0 5.0 - - - +
113G SER* 4.1 9.4 - - - +
115G PRO* 4.0 14.8 - - + -
143G HIS 5.4 0.7 - - - +
145G PHE* 3.9 25.8 - - + -
32H TRP* 3.7 18.4 - - + -
33H PHE* 1.3 74.3 - - - +
35H GLU* 1.3 59.2 + - - +
36H TYR* 3.9 19.1 - - + -
57H PHE 3.6 0.5 - - - +
58H TYR* 3.1 12.0 - - - -
59H ASN* 2.5 45.5 + - - +
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Residues in contact with GLU 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G GLN 4.0 0.2 - - - +
12G PHE* 3.1 5.0 - - - +
13G TYR 3.1 31.1 + - - +
66G ASN* 3.6 45.2 + - + +
69G ASN* 3.7 13.3 + - + +
70G LEU* 3.9 14.9 - - + +
73G MET* 3.3 22.4 - - - +
13H LYS* 2.7 31.7 + - - -
34H LEU* 1.3 72.9 - - - +
36H TYR* 1.3 61.8 + - - +
37H CYS* 5.8 0.7 - - - +
56H TYR* 4.5 9.1 - - - -
57H PHE 3.9 8.1 - - - +
58H TYR* 4.4 1.7 - - - -
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Residues in contact with TYR 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ALA* 4.4 10.7 - - + +
11G GLN 3.3 17.9 - - - -
12G PHE* 3.7 11.9 - + + -
137G PHE 5.6 0.2 + - - -
139G PRO* 3.4 20.6 - - - +
143G HIS 4.0 19.7 - - - -
144G LEU 4.6 2.2 + - - -
145G PHE* 3.4 39.7 - + - -
34H LEU* 3.9 17.9 - - + -
35H GLU* 1.3 77.2 - - - +
37H CYS* 1.3 64.0 + - - +
38H LYS* 3.4 40.7 + - + +
56H TYR* 3.6 1.7 - - - +
57H PHE* 2.7 64.5 + + + +
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Residues in contact with CYS 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G GLN 3.6 1.6 - - - +
10G ALA* 3.5 2.4 - - - -
11G GLN* 2.9 45.7 + - + +
66G ASN* 4.7 6.3 - - - +
10H GLU* 2.7 37.7 - - - +
35H GLU* 5.8 1.6 - - - +
36H TYR* 1.3 76.4 - - - +
38H LYS* 1.3 65.8 + - - +
39H SER* 4.4 6.3 - - - -
54H VAL* 4.0 15.9 - - - -
55H ARG 3.4 5.2 - - - +
56H TYR* 3.6 22.2 - - + -
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Residues in contact with LYS 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ILE* 4.0 13.9 - - + +
9G GLN 3.3 4.5 - - - -
10G ALA* 4.0 9.6 - - + -
139G PRO* 3.8 13.5 - - + -
140G ARG 2.8 21.0 + - - +
141G ASP 3.4 8.9 + - - -
142G ASP 2.7 26.1 + - - -
36H TYR* 3.4 30.9 + - + +
37H CYS* 1.3 78.8 - - - +
39H SER* 1.3 62.4 + - - +
40H GLU* 3.8 9.3 + - + +
53H LEU 3.6 2.4 - - - +
54H VAL* 3.4 1.2 - - - -
55H ARG* 2.8 48.8 + - + +
57H PHE* 3.5 24.7 - - + -
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Residues in contact with SER 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ILE 3.7 0.9 - - - +
8G ILE* 3.4 2.2 - - - -
9G GLN* 2.8 38.1 + - - +
8H PHE* 3.4 50.6 - - - +
10H GLU* 5.1 2.8 + - - -
37H CYS* 4.4 6.6 - - - -
38H LYS* 1.3 73.5 - - - +
40H GLU* 1.3 61.2 + - - +
52H LEU* 4.5 0.4 - - - -
53H LEU 3.6 3.8 - - - -
54H VAL* 3.7 22.7 - - - +
97H LYS* 5.2 0.7 + - - -
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Residues in contact with GLU 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G THR* 4.6 2.0 - - + -
7G ILE 3.3 3.4 - - - -
8G ILE* 3.9 32.8 - - + +
140G ARG 5.6 0.3 - - - +
141G ASP* 5.7 1.6 - - - -
38H LYS* 4.4 12.2 + - + +
39H SER* 1.3 75.2 - - - +
41H CYS* 1.3 62.6 + - - +
42H HIS* 3.0 32.2 + - + +
51H ARG 3.6 1.4 - - - +
52H LEU* 3.3 5.2 - - - +
53H LEU* 2.8 55.8 + - - +
55H ARG* 3.3 33.4 + - - -
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Residues in contact with CYS 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G THR* 3.2 9.2 - - - +
7G ILE* 2.7 42.7 + - + +
8H PHE* 3.4 23.1 - - - -
40H GLU* 1.3 72.7 - - - +
42H HIS* 1.3 60.7 + - - +
43H PHE* 3.6 23.0 - - + -
50H VAL* 4.8 0.4 - - + -
51H ARG 3.7 3.6 - - - -
104H VAL* 5.0 0.4 - - - -
105H CYS* 2.0 53.2 - - + -
108H ASN* 6.1 0.4 - - - -
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Residues in contact with HIS 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G HIS 3.9 2.7 - - - -
6G THR* 3.7 19.4 + - + -
40H GLU* 3.0 42.3 + - + +
41H CYS* 1.3 71.8 - - - +
43H PHE* 1.3 62.8 + - - +
44H TYR* 3.8 28.0 + - + +
49H ARG 3.6 1.0 - - - +
50H VAL* 3.2 7.8 - - - +
51H ARG* 2.8 62.1 + - + +
53H LEU* 4.2 15.0 - - + +
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Residues in contact with PHE 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G GLU 4.6 1.3 - - - +
4G GLU* 3.2 21.5 - - - +
5G HIS* 2.8 37.4 + - + +
7G ILE* 3.6 24.0 - - + -
41H CYS* 3.6 31.2 - - + -
42H HIS* 1.3 70.4 - - - +
44H TYR* 1.3 72.1 + - - +
46H GLY 3.5 14.8 - - - +
47H THR* 4.6 1.6 - - + -
49H ARG 3.7 1.6 - - - -
50H VAL* 3.6 32.3 - - + -
105H CYS 3.6 16.8 - - - -
106H ARG* 4.4 1.8 - - - -
109H TYR* 3.6 47.6 - + + -
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Residues in contact with TYR 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F ASP* 5.1 2.6 + - - -
70F VAL* 3.6 29.0 - - + +
74F ARG* 6.1 1.3 - - + -
3G GLU 4.0 0.9 - - - -
4G GLU* 3.8 27.4 - - + +
42H HIS* 3.8 36.4 + - + +
43H PHE* 1.3 80.0 - - - +
45H ASN* 1.3 77.5 + - - +
46H GLY 3.4 0.9 + - - +
48H GLN* 3.5 0.2 - - - +
49H ARG* 3.0 67.6 + - + +
51H ARG* 4.9 7.5 + - + -
316H NAG 3.5 31.6 - - + +
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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