Contacts of the strand formed by residues 29 - 36 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E ILE* 4.8 4.0 - - + -
20E LYS* 3.5 33.7 - - + +
21E GLY 3.4 8.7 - - - +
22E ARG* 4.6 14.6 - - - +
27E GLY 4.2 7.9 - - - +
28E GLN* 1.3 86.8 + - - +
30E VAL* 1.3 67.3 + - - +
81E GLU* 4.7 0.2 - - - -
82E PHE* 3.7 28.2 + - + +
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Residues in contact with VAL 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E TYR* 3.8 24.2 - - + -
20E LYS* 3.4 9.2 - - - +
21E GLY 2.7 57.0 + - - +
22E ARG* 4.6 0.7 - - - -
28E GLN* 3.7 19.7 - - + +
29E VAL* 1.3 81.5 - - - +
31E ALA* 1.3 59.5 + - - +
32E MET* 3.8 19.5 - - + -
67E GLN* 4.0 7.4 - - - +
79E ILE* 3.8 17.0 - - + -
80E PHE 3.4 13.7 - - - +
81E GLU* 5.1 0.2 - - - -
82E PHE* 3.8 8.7 - - - -
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Residues in contact with ALA 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ILE* 5.0 2.7 - - + -
18E VAL* 4.7 11.7 - - + -
19E TYR 3.4 6.1 - - - +
30E VAL* 1.3 73.8 - - - +
32E MET* 1.3 60.2 + - - +
78E LEU 3.6 1.2 - - - +
79E ILE* 3.7 1.6 - - - -
80E PHE* 2.8 51.8 + - + +
81E GLU 4.0 11.9 - - - +
82E PHE* 4.0 14.8 - - + +
83E LEU 5.4 0.7 - - - +
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Residues in contact with MET 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.7 35.7 - - + -
4E TYR* 4.3 15.9 - - + -
5E THR 4.7 1.1 - - - +
6E LYS* 3.9 24.2 - - + -
17E VAL 3.6 1.9 - - - +
18E VAL* 3.5 3.7 - - - +
19E TYR* 2.8 45.2 + - + +
20E LYS 4.6 1.3 - - - -
21E GLY* 3.9 26.0 - - - -
30E VAL* 3.8 12.8 - - + -
31E ALA* 1.3 76.4 - - - +
33E LYS* 1.3 62.2 + - - +
34E LYS* 3.7 0.8 + - + -
77E TYR* 4.8 5.6 - - + -
78E LEU 3.5 4.7 - - - -
79E ILE* 3.8 19.1 - - + -
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Residues in contact with LYS 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E GLY* 3.8 23.9 + - - -
15E TYR* 4.5 11.4 - - + -
16E GLY 4.5 10.1 - - - +
17E VAL 3.7 2.5 - - - +
18E VAL* 3.8 27.6 - - + +
31E ALA 4.2 0.4 - - - -
32E MET* 1.3 72.0 - - - +
34E LYS* 1.3 59.9 + - - +
35E ILE* 3.9 8.4 - - + +
76E LEU 3.5 1.0 - - - +
77E TYR* 3.4 4.8 - - - -
78E LEU* 2.9 46.4 + - + +
80E PHE* 3.7 24.4 - - + -
145E ALA* 5.7 1.8 - - - +
146E ASP* 2.8 36.9 + - - +
149E LEU* 5.0 1.8 - - + -
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Residues in contact with LYS 34 (chain E).
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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34D LYS* 6.5 1.1 - - - -
61D GLU* 5.5 6.7 - - - +
6E LYS* 3.7 24.5 - - - +
16E GLY* 3.3 20.8 - - - -
17E VAL* 3.1 39.5 + - + +
19E TYR* 4.8 12.1 - - + -
32E MET* 3.7 1.5 + - + +
33E LYS* 1.3 72.6 - - - +
35E ILE* 1.3 62.1 + - - +
36E ARG* 4.5 15.6 + - - +
75E ARG* 4.1 23.4 - - + +
76E LEU 3.7 2.9 - - - -
77E TYR* 3.6 32.3 - - + +
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Residues in contact with ILE 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E TYR* 4.2 21.3 - - + +
16E GLY* 4.0 14.4 - - - +
33E LYS* 4.4 9.0 - - + +
34E LYS* 1.3 81.0 - - - +
36E ARG* 1.3 69.8 + - - +
37E LEU* 3.6 8.2 + - + -
75E ARG* 3.3 4.4 - - - -
76E LEU* 2.7 57.7 + - + +
78E LEU* 3.8 32.8 - - + -
153E PHE* 4.5 21.5 - - + -
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Residues in contact with ARG 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C GLN* 3.4 24.9 + - - +
236C ASP* 2.5 42.0 + - - -
61D GLU* 3.6 18.2 + - - +
62D PRO* 3.5 29.7 - - - +
34E LYS* 4.4 11.3 - - - +
35E ILE* 1.3 77.2 - - - +
37E LEU* 1.3 69.7 - - - +
38E GLU* 3.9 3.8 + - - +
75E ARG* 3.4 28.2 - - + +
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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