Contacts of the strand formed by residues 29 - 36 (chain G) in PDB entry 4YC6
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 29 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7G ILE* 4.8 3.8 - - + -
20G LYS* 3.5 32.8 - - + +
21G GLY 3.5 9.4 - - - +
22G ARG* 4.6 14.1 - - - +
27G GLY 4.2 8.3 - - - +
28G GLN* 1.3 86.4 + - - +
30G VAL* 1.3 65.6 + - - +
82G PHE* 3.0 34.0 + - + +
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Residues in contact with VAL 30 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4G TYR* 3.9 22.0 - - + -
20G LYS* 3.3 9.5 - - - +
21G GLY* 2.7 59.9 + - - +
22G ARG* 4.5 0.7 - - - -
28G GLN* 3.7 9.6 - - + +
29G VAL* 1.3 81.1 - - - +
31G ALA* 1.3 57.3 + - - +
32G MET* 3.8 15.9 - - + -
67G GLN* 3.7 22.7 - - - +
79G ILE* 3.7 12.1 - - + -
80G PHE 2.9 19.7 - - - +
82G PHE* 3.7 7.6 - - - +
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Residues in contact with ALA 31 (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 ILE* 5.1 2.0 - - + -
18G VAL* 4.6 12.8 - - + -
19G TYR 3.4 5.4 - - - -
30G VAL* 1.3 74.1 - - - +
32G MET* 1.3 60.6 + - - +
33G LYS 4.1 0.4 - - - -
78G LEU 3.6 1.0 - - - +
79G ILE* 3.7 1.7 - - - -
80G PHE* 2.8 46.4 + - + +
81G GLU 4.0 10.8 - - - +
82G PHE* 4.0 17.5 - - + +
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Residues in contact with MET 32 (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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1G MET* 3.6 35.7 - - + -
4G TYR* 4.3 15.3 - - + -
5G THR 4.7 1.3 - - - +
6G LYS* 3.9 23.6 - - + -
17G VAL 3.6 1.2 - - - +
18G VAL* 3.5 3.2 - - - +
19G TYR* 2.7 47.9 + - + +
20G LYS 4.5 1.6 - - - -
21G GLY* 3.8 26.9 - - - -
30G VAL* 3.8 12.6 - - + -
31G ALA* 1.3 76.6 - - - +
33G LYS* 1.3 63.2 + - - +
34G LYS* 3.7 0.7 + - + -
77G TYR* 4.8 7.6 - - + -
78G LEU 3.4 4.3 - - - -
79G ILE* 3.7 20.0 - - + -
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Residues in contact with LYS 33 (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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13G GLY* 3.7 24.4 + - - -
15G TYR* 4.5 11.2 - - + -
16G GLY 4.5 10.1 - - - +
17G VAL 3.7 2.9 - - - +
18G VAL* 3.9 27.7 - - + +
31G ALA 4.1 0.8 - - - -
32G MET* 1.3 71.0 - - - +
34G LYS* 1.3 60.1 + - - +
35G ILE* 4.4 8.4 - - + +
76G LEU 3.5 2.1 - - - +
77G TYR* 3.4 5.0 - - - -
78G LEU* 2.9 49.3 + - + +
80G PHE* 3.7 24.4 - - + -
145G ALA* 5.8 1.4 - - - +
146G ASP* 2.8 35.4 + - - +
149G LEU* 5.1 1.6 - - + -
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Residues in contact with LYS 34 (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 LYS* 3.9 21.5 - - - +
16G GLY* 3.3 19.8 - - - -
17G VAL* 3.0 40.8 + - + +
19G TYR* 4.6 13.2 - - + -
32G MET* 3.7 1.3 + - + +
33G LYS* 1.3 71.7 - - - +
35G ILE* 1.3 60.7 + - - +
36G ARG* 4.6 13.9 - - - +
75G ARG* 4.1 24.3 - - - +
76G LEU 3.7 2.7 - - - -
77G TYR* 3.6 34.5 - - + +
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Residues in contact with ILE 35 (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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15G TYR* 4.2 21.5 - - + +
16G GLY* 4.0 16.6 - - - +
33G LYS* 4.4 9.6 - - + +
34G LYS* 1.3 80.8 - - - +
36G ARG* 1.3 69.3 + - - +
37G LEU* 4.8 8.5 - - + -
75G ARG* 3.4 4.6 - - - -
76G LEU* 2.7 59.7 + - + +
78G LEU* 3.8 33.9 - - + -
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Residues in contact with ARG 36 (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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235A GLN* 3.3 27.7 + - - +
236A ASP* 3.0 30.5 + - - -
61B GLU* 3.4 32.1 + - - +
62B PRO* 4.2 17.5 - - - +
34G LYS* 4.3 13.0 - - - +
35G ILE* 1.3 76.7 - - - +
37G LEU* 1.3 68.9 + - - +
38G GLU* 3.9 4.3 + - - +
74G SER 4.8 1.3 - - - +
75G ARG* 3.4 29.4 - - + +
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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