Contacts of the strand formed by residues 66 - 77 (chain G) in PDB entry 5IYB
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 VAL 66 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1475A LEU* 3.9 23.1 - - + -
72F GLN* 6.2 0.2 - - - +
11G ILE 3.8 1.0 - - - +
12G LEU* 3.9 3.6 - - - +
13G LEU* 3.1 65.5 + - + +
18G PHE* 3.6 15.3 - - + -
57G GLY* 3.8 33.2 - - - +
58G VAL 3.8 4.7 - - - +
59G ILE* 4.7 5.2 - - + +
64G GLY 3.8 1.6 + - - -
65G PHE* 1.3 74.5 - - - +
67G LEU* 1.3 62.5 + - - +
68G TYR* 3.7 10.5 - - + -
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Residues in contact with LEU 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU 6.1 0.7 - - - +
10G GLU* 3.5 45.1 - - + +
11G ILE 3.4 19.1 - - - +
12G LEU* 4.2 13.9 - - + +
57G GLY* 3.6 0.7 - - - -
58G VAL* 3.0 37.1 + - + +
60G GLN* 3.4 33.2 - - + +
65G PHE 4.1 0.6 + - - -
66G VAL* 1.3 72.2 - - - +
68G TYR* 1.3 62.3 + - - +
69G PRO* 3.4 9.8 - - + +
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Residues in contact with TYR 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1475A LEU* 3.9 25.4 + - - +
1477A ALA* 4.8 8.3 + - - +
10G GLU* 4.6 1.1 - - - -
11G ILE* 2.9 41.6 + - + +
13G LEU* 3.8 20.4 - - + -
22G LEU* 4.2 17.9 - - + +
23G LEU* 5.6 7.6 - - + -
26G VAL* 4.3 15.7 - - + -
54G ILE* 3.6 21.8 - - + -
55G GLY 3.5 18.8 - - - -
57G GLY* 3.7 22.2 - - - -
66G VAL* 3.7 31.6 - - + -
67G LEU* 1.3 71.1 - - - +
69G PRO* 1.3 66.2 - - - +
70G VAL* 3.5 6.0 - - + +
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Residues in contact with PRO 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G GLU* 6.0 2.5 - - - +
9G HIS 3.7 6.3 - - - +
10G GLU* 4.4 13.6 - - + -
54G ILE* 3.5 1.9 - - - +
55G GLY* 2.6 50.6 + - - -
56G ALA 3.5 15.3 - - - +
58G VAL* 5.9 1.8 - - + -
67G LEU* 3.4 13.5 - - + +
68G TYR* 1.3 85.1 - - - +
70G VAL* 1.3 57.7 + - - +
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Residues in contact with VAL 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G GLU* 3.4 8.8 - - - +
9G HIS 2.9 32.9 + - - +
11G ILE* 3.7 21.3 - - + -
26G VAL* 4.9 4.5 - - + -
30G LEU* 3.7 24.7 - - + -
51G ILE* 4.0 8.7 - - + -
53G ASN 3.4 9.4 - - - +
54G ILE* 4.0 22.0 - - + -
68G TYR* 3.5 15.0 - - + +
69G PRO* 1.3 79.3 - - - +
71G LYS* 1.3 75.5 + - - +
72G TYR* 3.9 6.3 - - + -
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Residues in contact with LYS 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G LEU 3.8 4.5 - - - +
8G GLU* 3.2 33.0 - - + +
51G ILE* 3.6 3.5 - - - +
52G ASP* 2.7 53.9 + - + +
53G ASN* 2.6 37.5 + - + +
70G VAL* 1.3 75.6 - - - +
72G TYR* 1.3 56.3 + - - +
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Residues in contact with TYR 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G SER* 3.5 4.3 - - - -
7G LEU* 3.1 68.0 + - + +
8G GLU 3.9 20.5 + - - -
9G HIS* 3.9 14.5 - - + +
30G LEU* 4.7 8.1 - - + -
34G VAL* 5.2 11.5 - - + +
45G VAL* 5.7 4.3 - - + +
48G VAL* 3.8 26.0 - - + -
50G THR 3.4 13.7 - - - +
51G ILE* 4.1 9.6 - - + -
52G ASP* 3.8 4.0 - - - +
70G VAL* 3.9 14.4 - - + -
71G LYS* 1.3 76.6 - - - +
73G LYS* 1.3 61.8 + - - +
74G ALA* 3.7 28.9 - - + -
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Residues in contact with LYS 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G HIS* 4.1 19.5 + - + +
5G ILE 3.3 7.4 - - - +
6G SER* 3.3 25.4 + - - +
48G VAL* 3.7 1.4 - - - +
49G THR* 2.6 35.9 + - - +
50G THR* 2.9 31.5 + - - +
52G ASP* 4.7 16.8 - - + +
72G TYR* 1.3 75.9 - - - +
74G ALA* 1.3 57.8 + - - +
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Residues in contact with ALA 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G HIS* 3.4 4.5 + - - -
5G ILE* 2.8 39.2 + - - +
7G LEU* 4.9 9.2 - - + -
45G VAL* 5.1 5.2 - - + -
47G ALA 3.3 13.9 - - - +
48G VAL* 3.9 6.1 - - + -
49G THR* 4.0 1.3 - - - +
72G TYR* 3.7 27.5 + - + -
73G LYS* 1.3 75.7 - - - +
75G ILE* 1.3 67.4 + - - +
76G VAL* 3.9 4.7 + - + -
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Residues in contact with ILE 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 4.0 13.5 - - + -
37D VAL* 4.6 15.0 - - + -
40D LEU* 3.6 37.5 - - + -
41D LEU* 4.8 6.3 - - + -
2G PHE* 5.3 3.1 - - + -
3G TYR 3.2 12.1 - - - +
4G HIS* 3.9 9.6 - - + -
45G VAL* 4.0 0.9 - - - +
46G ILE* 3.0 41.4 + - + +
47G ALA* 2.7 30.8 + - + +
49G THR* 3.6 22.2 - - + -
74G ALA* 1.3 72.5 - - - +
76G VAL* 1.3 66.8 + - - +
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Residues in contact with VAL 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D PHE* 4.7 4.5 - - + -
1G MET 3.7 0.2 - - - +
2G PHE* 3.7 2.5 - - - -
3G TYR* 2.8 59.3 + - + +
5G ILE* 3.5 37.7 - - + -
7G LEU* 4.3 13.7 - - + -
42G TYR* 3.8 22.2 - - + +
44G PHE 3.8 6.7 - - - +
45G VAL* 4.8 10.1 - - + -
46G ILE* 4.6 2.5 - - - -
74G ALA* 3.9 6.0 + - + +
75G ILE* 1.3 79.8 - - - +
77G PHE* 1.3 59.9 + - - +
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Residues in contact with PHE 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D TYR* 6.1 1.8 - + - -
1G MET* 3.2 37.2 - - - -
2G PHE* 3.3 36.3 - + + -
42G TYR 3.1 12.5 - - - +
43G GLY* 3.4 13.2 - - - -
44G PHE* 3.3 20.9 + + + +
46G ILE* 4.5 10.1 - - + -
76G VAL* 1.3 75.2 - - - +
78G ARG* 1.3 59.3 + - - +
79G PRO* 3.7 15.6 - - + +
85G VAL* 6.2 3.4 - - + -
101G ILE* 4.2 28.7 - - + -
102G GLY* 6.3 0.2 - - - -
103G PRO* 5.8 4.5 - - + -
104G MET* 3.6 34.8 - - + -
157G ILE* 5.1 0.9 - - - +
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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