Contacts of the strand formed by residues 78 - 86 (chain R) in PDB entry 4M8B
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 78 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11R ILE* 3.4 30.5 - - + -
12R ASP 3.8 21.8 - - - -
13R ASP* 4.4 7.2 - - - -
14R GLU* 5.4 1.6 - - + -
17R LEU* 3.5 31.0 - - + -
74R ILE* 3.6 8.9 - - - +
75R SER* 3.0 42.4 + - - +
76R GLY* 5.5 0.2 - - - -
77R LYS* 1.3 87.0 - - + +
79R LEU* 1.3 68.1 + - - +
80R VAL* 4.8 0.2 - - + -
119R LYS* 3.9 32.8 - - + -
120R THR 3.4 18.2 - - - +
121R PHE* 3.8 12.3 - + + -
140R LEU* 5.3 2.5 - - + -
181R VAL* 5.5 0.2 - - - -
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Residues in contact with LEU 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A T 3.6 12.8 - - + -
11A G 3.4 39.0 - - + +
12A T 5.1 1.1 - - + -
72R SER* 4.3 12.3 - - - +
73R ARG 3.4 11.9 - - - +
74R ILE* 4.2 16.8 - - + -
77R LYS 4.2 0.4 + - - +
78R PHE* 1.3 78.5 - - - +
80R VAL* 1.3 60.3 + - - +
81R TYR* 3.4 27.7 - - + +
118R LYS 3.7 0.5 - - - +
119R LYS* 3.0 7.1 - - - +
120R THR* 2.9 47.1 + - - +
181R VAL* 4.2 15.9 - - + -
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Residues in contact with VAL 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R SER* 4.7 0.2 + - - -
71R PRO 4.1 1.6 - - - +
72R SER* 3.6 1.9 - - - -
73R ARG* 2.8 40.5 + - + +
74R ILE 5.7 0.2 - - - -
75R SER* 3.8 28.3 - - - -
78R PHE* 4.8 2.5 - - + -
79R LEU* 1.3 79.6 - - - +
81R TYR* 1.3 79.5 + - - +
82R ARG* 5.1 3.6 - - + -
117R LEU* 4.4 10.8 - - + -
118R LYS 3.3 7.0 - - - +
119R LYS* 4.2 15.5 - - + +
144R TYR* 4.1 15.9 - - - +
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Residues in contact with TYR 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A G 4.5 7.4 - + + +
10A T 3.9 38.5 + - + +
69R TRP* 3.8 27.7 - + + -
70R SER* 3.5 22.7 - - - +
72R SER* 3.4 30.2 - - - -
79R LEU* 3.4 39.5 - - + +
80R VAL* 1.3 76.2 - - - +
82R ARG* 1.3 65.3 + - - +
117R LEU* 3.5 9.4 - - - +
118R LYS* 2.9 52.7 + - + +
120R THR* 3.9 16.8 + - + -
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Residues in contact with ARG 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R TRP* 3.3 5.0 - - - -
70R SER* 2.7 44.3 + - - +
80R VAL* 5.1 4.3 - - + -
81R TYR* 1.3 76.0 - - - +
83R GLU* 1.3 63.8 + - - +
84R TYR* 3.7 2.4 + - - -
101R TYR 5.6 1.6 + - - -
102R ASN* 4.0 11.5 + - - +
113R TYR* 3.0 62.9 - - + +
116R LEU 4.0 3.6 - - - +
117R LEU* 3.4 26.2 - - + -
146R GLU* 3.2 21.5 + - - -
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Residues in contact with GLU 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67R PHE* 3.3 35.6 - - + -
68R SER 3.1 16.6 + - - +
69R TRP* 3.5 15.4 - - + -
82R ARG* 1.3 73.5 - - - +
84R TYR* 1.3 65.6 + - - +
85R ASN* 4.0 15.0 + - - +
113R TYR* 3.4 8.0 - - - +
114R THR* 2.5 58.1 + - - +
115R GLY 4.5 0.7 + - - -
116R LEU* 3.3 31.7 + - + +
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Residues in contact with TYR 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A A 5.8 0.5 + - - -
68R SER* 3.2 33.0 + - - +
69R TRP 3.2 39.2 + - - -
70R SER* 3.9 8.7 - - - -
71R PRO* 5.9 0.4 - - + -
82R ARG 4.0 1.3 - - - -
83R GLU* 1.3 75.3 - - - +
85R ASN* 1.3 74.1 + - - +
104R PHE* 4.0 23.8 - + + -
111R TYR* 4.2 31.0 - + - -
112R PHE 3.0 13.0 - - - +
113R TYR* 3.9 13.7 - + + -
114R THR* 4.4 0.7 - - - -
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Residues in contact with ASN 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68R SER* 5.0 2.8 + - - -
83R GLU* 4.0 13.6 + - - +
84R TYR* 1.3 83.9 - - - +
86R ARG* 1.3 63.5 + - + +
111R TYR* 3.1 12.1 - - - +
112R PHE* 2.8 55.0 + - + -
114R THR* 3.6 19.7 - - - +
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Residues in contact with ARG 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85R ASN* 1.3 78.3 - - + +
87R LEU* 1.3 72.0 + - - +
96R HIS* 5.2 0.5 + - - -
109R ARG* 5.2 12.9 - - + +
110R LYS 3.6 8.7 - - - +
111R TYR* 3.5 29.5 + - + -
112R PHE* 3.5 11.6 - - - -
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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