Contacts of the strand formed by residues 2 - 13 (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 PHE 2 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 3.0 45.6 + - + +
34D ASN* 3.0 31.9 - - - -
37D VAL* 3.5 32.5 - - + -
64D THR* 4.6 19.3 - - + -
67D TYR* 4.4 20.6 - + - -
68D THR* 4.2 8.7 - - - -
102D ASN* 5.4 2.9 - - - -
1G MET* 1.3 82.9 - - - +
3G TYR* 1.3 69.1 + - - +
46G ILE* 5.2 2.7 - - + -
75G ILE* 5.3 4.9 - - + -
76G VAL 3.7 3.1 - - - -
77G PHE* 3.3 38.1 - + + -
102G GLY* 5.7 2.5 - - - -
103G PRO* 6.3 0.4 - - + -
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Residues in contact with TYR 3 (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* 4.4 19.7 - + + +
29D ALA* 4.0 19.5 - - + -
30D GLU 3.1 19.3 - - - +
31D THR* 4.0 11.2 - - + -
32D LEU* 3.3 12.1 - - - +
95D PHE* 4.2 5.1 - + - -
1G MET* 3.5 40.3 - - + +
2G PHE* 1.3 84.8 - - - +
4G HIS* 1.3 60.5 + - - +
5G ILE* 4.1 8.1 - - + -
75G ILE* 3.2 7.8 - - - +
76G VAL* 2.8 51.6 + - + +
78G ARG* 3.7 26.2 + - + -
80G PHE* 3.1 30.5 - + - -
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Residues in contact with HIS 4 (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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30D GLU* 3.0 38.8 + - + +
32D LEU* 3.8 21.3 - - + +
40D LEU* 5.5 3.3 - - + +
3G TYR* 1.3 74.7 - - - +
5G ILE* 1.3 61.7 + - - +
49G THR* 2.9 45.1 + - + +
50G THR* 5.3 0.2 - - - -
73G LYS* 4.1 25.0 - - + +
74G ALA 3.4 12.3 - - - -
75G ILE* 3.9 7.9 - - + -
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Residues in contact with ILE 5 (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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25D GLU 5.2 3.6 - - - +
26D PHE* 4.4 15.5 - - + -
29D ALA* 3.7 33.2 - - + -
3G TYR* 4.1 9.2 - - + -
4G HIS* 1.3 80.4 - - - +
6G SER* 1.3 65.6 + - - +
7G LEU* 3.6 33.7 - - + -
42G TYR* 4.5 4.5 - - + -
73G LYS* 3.3 6.3 - - - +
74G ALA* 2.8 39.1 + - - +
76G VAL* 3.5 32.1 - - + -
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Residues in contact with SER 6 (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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5G ILE* 1.3 77.0 - - - +
7G LEU* 1.3 72.5 + - - +
72G TYR 3.5 8.3 - - - -
73G LYS* 3.3 28.2 + - - +
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Residues in contact with LEU 7 (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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5G ILE* 3.6 29.1 + - + +
6G SER* 1.3 84.2 - - - +
8G GLU* 1.3 70.6 - - - +
42G TYR* 3.5 45.1 - - + +
45G VAL* 5.7 7.2 - - + -
71G LYS* 3.8 1.9 - - - +
72G TYR* 3.1 63.8 + - + +
74G ALA* 4.9 3.1 - - + -
76G VAL* 4.3 12.8 - - + -
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Residues in contact with GLU 8 (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* 1.3 82.5 - - - +
9G HIS* 1.3 67.0 + - - +
69G PRO* 6.0 2.4 - - - +
70G VAL 3.4 6.1 - - - +
71G LYS* 3.2 40.5 - - + -
72G TYR* 3.9 6.9 + - - -
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Residues in contact with HIS 9 (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* 1.3 79.7 - - - +
10G GLU* 1.3 90.8 + - - +
11G ILE* 3.6 16.7 + - + +
30G LEU* 5.6 1.5 - - + +
33G GLU* 3.7 22.1 + - - -
34G VAL* 4.0 22.9 - - + +
69G PRO* 3.7 1.1 - - - +
70G VAL* 2.9 35.9 + - + +
72G TYR* 3.9 19.7 - - + +
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Residues in contact with GLU 10 (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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14A PRO* 5.1 3.1 - - - +
15A LEU 4.5 2.6 - - - +
16A ARG* 2.9 44.4 + - - -
9G HIS* 1.3 102.2 + - - +
11G ILE* 1.3 59.5 + - - +
12G LEU 4.1 1.4 + - - -
33G GLU* 4.8 1.0 - - - +
67G LEU* 3.5 38.4 - - + +
68G TYR 3.8 3.1 - - - -
69G PRO* 4.6 13.5 - - + -
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Residues in contact with ILE 11 (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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9G HIS* 3.6 19.3 - - + +
10G GLU* 1.3 73.3 - - - +
12G LEU* 1.3 71.5 + - - +
13G LEU* 4.8 6.1 - - + +
26G VAL* 4.1 24.2 - - + +
29G LYS* 5.3 8.1 - - + -
30G LEU* 4.0 32.8 - - + -
33G GLU* 3.5 23.6 - - - +
34G VAL* 4.9 0.9 - - + -
66G VAL 3.8 0.9 - - - +
67G LEU* 3.4 5.7 - - - +
68G TYR* 2.9 42.8 + - + +
70G VAL* 3.7 23.1 - - + -
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Residues in contact with LEU 12 (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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10G GLU 4.1 2.0 + - - +
11G ILE* 1.3 79.4 - - - +
13G LEU* 1.3 62.9 + - - +
29G LYS* 3.2 25.6 + - - +
33G GLU* 5.1 3.5 + - - +
60G GLN* 5.1 5.2 - - + -
63G ARG* 4.1 24.7 - - - +
65G PHE* 3.5 44.6 - - + -
66G VAL 3.9 7.9 - - - +
67G LEU* 4.2 15.7 - - + +
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Residues in contact with LEU 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ILE* 4.8 4.7 - - + +
12G LEU* 1.3 77.9 - - - +
14G HIS* 1.3 71.2 + - - +
15G PRO 3.7 0.9 - - - -
17G TYR* 4.0 29.6 - - + +
18G PHE* 4.2 6.7 - - + -
22G LEU* 3.5 32.3 - - + -
25G THR* 5.1 5.8 - - + -
26G VAL* 4.0 13.2 - - + -
29G LYS* 4.4 14.6 - - + +
65G PHE* 3.7 5.1 - - - -
66G VAL* 3.1 55.8 + - + +
68G TYR* 3.8 11.9 - - + -
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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