Contacts of the strand formed by residues 110 - 117 (chain E) in PDB entry 6S1M
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 110 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ASP* 6.1 0.9 - - - -
103E PHE 4.2 0.2 - - - +
105E ALA* 3.3 36.3 + - + +
108E GLN* 3.1 3.6 - - - -
109E GLU* 1.3 88.6 + - - +
111E VAL* 1.3 70.4 + - - +
112E SER* 3.9 10.3 - - - +
143F GLU* 3.9 27.3 + - + +
146F ARG* 4.4 18.6 - - - +
147F ILE* 4.2 15.8 - - - +
150F ASP* 4.4 5.8 + - - -
180F ILE* 3.5 31.9 - - + -
181F LYS 3.1 5.2 - - - +
182F LEU* 3.6 15.0 - - + -
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Residues in contact with VAL 111 (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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102E VAL* 3.7 27.6 - - + -
103E PHE 3.4 6.1 - - - +
104E GLU* 4.4 14.6 - - + -
108E GLN* 5.0 7.9 - - + +
109E GLU 5.5 0.2 - - - -
110E LYS* 1.3 82.8 - - - +
112E SER* 1.3 68.7 + - - +
113E ASP* 5.4 3.0 - - + +
179F ASN 3.7 1.2 - - - +
180F ILE* 3.3 1.7 - - - -
181F LYS* 2.8 47.6 + - + +
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Residues in contact with SER 112 (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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81E CYS 4.7 5.0 + - - -
102E VAL* 3.2 8.3 - - - +
103E PHE* 2.8 46.6 + - - +
110E LYS* 3.9 11.1 - - - -
111E VAL* 1.3 77.9 - - - +
113E ASP* 1.3 60.3 + - - +
114E TYR* 3.5 25.0 + - - -
150F ASP* 5.6 0.5 + - - -
179F ASN 3.3 5.8 - - - -
180F ILE* 3.7 21.1 - - - +
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Residues in contact with ASP 113 (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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91E ARG* 4.3 6.1 + - - -
100E ALA* 4.5 0.3 - - - +
101E LEU 3.5 2.8 - - - +
102E VAL* 3.3 25.9 - - + +
111E VAL* 5.4 3.4 - - + +
112E SER* 1.3 75.8 - - - +
114E TYR* 1.3 63.0 + - - +
115E GLU* 2.8 33.8 - - - +
178F GLY* 2.9 3.1 - - - -
179F ASN* 2.7 58.9 + - - +
181F LYS* 6.4 0.4 - - - -
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Residues in contact with TYR 114 (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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78E ILE* 3.8 25.4 - - + -
81E CYS* 3.3 26.2 + - + +
99E LEU 3.7 0.5 - - - +
100E ALA* 3.2 2.4 - - - -
101E LEU* 2.5 46.7 + - + +
103E PHE* 3.7 27.1 - + - -
112E SER* 3.5 24.2 + - - -
113E ASP* 1.3 78.5 - - - +
115E GLU* 1.3 64.4 + - - +
116E MET 3.8 0.8 + - - -
150F ASP* 3.7 14.4 - - - +
151F LEU* 4.3 4.8 - - + +
154F ILE* 3.6 37.2 - - + -
177F ASN 3.5 3.6 - - - +
178F GLY* 3.6 20.2 - - - -
179F ASN 5.0 0.9 - - - -
180F ILE* 4.0 16.7 - - + +
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Residues in contact with GLU 115 (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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78E ILE* 5.1 1.0 - - - +
91E ARG* 5.1 1.7 + - - -
98E THR* 4.2 14.5 + - - +
99E LEU 3.4 4.5 - - - -
100E ALA* 3.6 19.5 - - - +
113E ASP* 2.8 38.8 - - - +
114E TYR* 1.3 72.7 - - - +
116E MET* 1.3 61.0 + - - +
117E LYS* 5.3 0.2 - - - +
175F LEU 4.2 0.3 - - - +
176F GLY* 3.4 4.7 - - - -
177F ASN* 2.7 52.1 + - - +
178F GLY* 5.6 0.2 - - - -
179F ASN* 6.1 0.9 - - - +
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Residues in contact with MET 116 (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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70E VAL* 3.6 29.4 - - + -
71E ASN* 4.7 1.1 - - + +
74E SER* 4.7 8.1 - - - -
75E MET* 3.5 43.5 - - + -
78E ILE* 3.5 24.5 - - + -
98E THR* 3.3 4.0 - - - -
99E LEU* 2.7 72.0 + - + +
101E LEU* 4.2 8.5 - - + -
114E TYR 3.8 0.8 + - - -
115E GLU* 1.3 73.2 - - - +
117E LYS* 1.3 70.8 + - - +
118E LEU* 3.5 5.0 + - + +
175F LEU* 4.3 6.3 - - - +
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Residues in contact with LYS 117 (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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70E VAL* 5.9 0.5 - - - +
71E ASN* 5.6 5.4 + - - +
97E ASP 4.1 5.6 - - - +
98E THR* 4.6 4.3 - - - +
115E GLU 4.0 1.0 + - - +
116E MET* 1.3 80.1 - - - +
118E LEU* 1.3 68.6 + - - +
119E MET* 5.0 7.8 - - + +
173F GLY 3.8 8.8 + - - -
174F GLU* 3.4 28.1 + - - +
175F LEU* 4.6 2.4 + - - -
176F GLY* 3.9 23.6 - - - +
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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