Contacts of the strand formed by residues 94 - 103 (chain E) in PDB entry 6NIL
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 LYS 94 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88E LEU* 4.1 5.5 - - - +
90E ARG* 5.1 0.3 - - - +
91E GLU* 2.9 43.5 + - + +
92E ALA 3.4 1.7 - - - +
93E GLY* 1.3 79.6 - - - +
95E VAL* 1.3 70.9 + - - +
96E TYR* 3.6 36.1 + - + +
113E TRP* 3.6 40.0 - - - -
114E ILE 3.8 11.2 - - - +
115E ASP* 4.9 7.2 - - - +
116E LEU* 4.0 9.1 - - - +
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Residues in contact with VAL 95 (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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44E PHE* 3.8 23.6 - - + -
48E CYS* 4.7 10.1 - - + -
86E VAL* 5.6 0.9 - - + -
87E ASP 3.3 21.3 - - - +
88E LEU* 3.7 27.6 - - + -
94E LYS* 1.3 78.7 - - - +
96E TYR* 1.3 66.5 + - - +
97E LEU* 4.0 8.2 - - + +
114E ILE* 3.6 47.5 + - + +
116E LEU* 3.7 14.1 - - + -
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Residues in contact with TYR 96 (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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85E TYR* 3.6 12.6 - - + +
87E ASP* 3.3 24.5 + - - +
90E ARG* 3.4 53.9 - - + +
91E GLU* 3.2 39.5 + - - -
94E LYS* 3.6 23.9 + - - -
95E VAL* 1.3 77.2 - - - +
97E LEU* 1.3 67.2 + - - +
112E GLY 4.1 2.2 - - - +
113E TRP* 3.5 33.0 - + + -
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Residues in contact with LEU 97 (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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44E PHE* 5.5 0.7 - - + -
48E CYS* 6.3 0.2 - - - -
55E ILE* 4.4 0.9 - - + -
57E PHE* 3.7 26.7 - - + -
68E PHE* 4.2 14.6 - - + -
85E TYR* 3.7 8.2 + - - +
86E VAL* 3.7 37.5 - - + -
95E VAL* 4.0 12.3 - - + +
96E TYR* 1.3 83.7 - - - +
98E LYS* 1.3 62.4 + - - +
110E TRP* 4.1 17.7 - - + -
111E LYS* 3.3 3.2 - - - +
112E GLY 2.9 38.8 + - - +
114E ILE* 3.7 29.2 - - + -
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Residues in contact with LYS 98 (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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68E PHE* 4.9 1.9 - - - -
83E ARG* 3.2 30.6 + - - +
85E TYR* 3.1 67.1 + - + +
97E LEU* 1.3 77.9 - - - +
99E ALA* 1.3 65.2 + - - +
109E ILE* 3.5 26.8 - - + +
110E TRP* 3.3 6.5 - - - +
111E LYS* 3.7 37.2 - - + +
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Residues in contact with ALA 99 (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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68E PHE* 3.6 28.3 - - + -
84E GLU* 4.1 9.9 - - + +
98E LYS* 1.3 78.4 - - - +
100E PRO* 1.3 67.3 - - + +
101E MET* 4.6 1.7 - - + +
109E ILE* 3.6 4.0 - - - -
110E TRP* 2.6 47.7 + - + +
7F VAL* 3.8 17.5 - - + -
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Residues in contact with PRO 100 (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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83E ARG* 3.9 21.1 - - + -
84E GLU* 3.8 30.5 - - + +
99E ALA* 1.3 85.7 - - - +
101E MET* 1.3 64.3 + - - +
107E CYS* 4.9 9.6 - - - -
108E VAL 4.5 0.7 - - - +
109E ILE* 3.7 28.5 - - + -
128E ASP* 4.3 7.4 - - - +
7F VAL* 3.4 15.8 - - - +
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Residues in contact with MET 101 (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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21E LEU* 6.5 0.2 - - - -
66E LEU* 3.7 28.0 - - + -
99E ALA* 4.6 4.0 - - + +
100E PRO* 1.3 77.1 - - - +
102E ILE* 1.3 72.6 + - - +
103E LEU* 3.7 35.7 - - + -
107E CYS* 3.4 7.5 - - - -
108E VAL* 2.9 41.3 + - + +
110E TRP* 3.8 26.2 - - + -
125E LEU* 5.0 6.3 - - + -
7F VAL* 3.9 20.6 - - + -
9F ILE* 4.7 13.9 - - + +
97F GLN* 4.9 8.3 - - - +
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Residues in contact with ILE 102 (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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101E MET* 1.3 83.8 - - - +
103E LEU* 1.3 56.0 + - - +
105E GLY 3.5 24.9 - - - +
106E VAL 3.3 6.3 - - - +
107E CYS* 4.6 10.1 - - + +
94F TYR* 3.8 14.4 - - + +
95F SER* 3.6 21.5 - - - +
96F THR* 2.7 37.9 + - - +
97F GLN* 2.9 19.2 + - - +
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Residues in contact with LEU 103 (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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17E PHE* 3.7 20.6 - - + -
18E PHE* 3.4 23.6 - - + -
21E LEU* 4.6 21.1 - - + -
101E MET* 3.7 31.5 - - + -
102E ILE* 1.3 71.5 - - - +
104E ASN* 1.3 99.5 + - - +
105E GLY 3.2 0.4 - - - -
106E VAL* 2.9 27.2 + - - +
108E VAL* 5.1 4.7 - - + -
125E LEU* 4.6 8.1 - - + -
9F ILE* 4.4 18.6 - - + -
97F GLN* 3.3 11.7 - - + +
98F VAL* 5.8 0.7 - - - -
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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