Contacts of the strand formed by residues 166 - 173 (chain E) in PDB entry 3HN3
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 LEU 166 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ARG 3.7 0.9 - - - +
104E GLU* 3.2 4.6 - - - -
105E VAL* 2.7 45.3 + - + +
107E LEU* 4.0 33.7 - - + +
134E VAL* 3.0 36.8 - - + -
135E ASN* 3.7 9.9 - - - +
153E ILE* 4.0 17.7 - - + -
157E VAL* 3.7 15.9 - - + -
165E ARG* 1.3 69.7 - - - +
167E ARG* 1.3 60.8 + - - +
168E ILE* 3.8 29.4 - - + -
220E LEU* 4.1 7.4 - - + -
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Residues in contact with ARG 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E TYR 3.1 28.5 + - - -
65E ARG 3.4 18.0 + - - -
66E ARG* 3.4 14.3 + - - +
67E PRO* 3.9 18.4 - - - +
102E GLU* 2.9 47.3 + - + -
103E ARG 3.6 3.1 - - - -
104E GLU* 3.9 22.0 - - + -
133E TRP 3.7 1.0 - - - +
134E VAL* 3.5 6.1 - - - +
135E ASN* 2.9 44.6 + - - +
136E GLY* 3.5 19.2 - - - +
165E ARG 3.4 2.4 + - - +
166E LEU* 1.3 71.4 - - - +
168E ILE* 1.3 60.8 + - - +
169E THR* 3.2 12.0 + - - +
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Residues in contact with ILE 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E LEU* 3.5 31.9 - - + -
45E TRP* 4.0 16.1 - - + -
102E GLU* 3.2 6.3 - - - +
103E ARG* 2.9 35.8 + - + +
105E VAL* 4.0 8.7 - - + -
121E LEU* 3.9 35.0 - - + -
132E VAL* 4.2 4.3 - - + -
133E TRP 3.6 4.0 - - - +
134E VAL* 5.1 2.5 - - + -
166E LEU* 3.8 31.2 - - + -
167E ARG* 1.3 74.4 - - - +
169E THR* 1.3 62.1 + - - +
170E ILE* 4.0 20.4 - - + -
220E LEU* 4.7 0.4 - - + -
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Residues in contact with THR 169 (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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64E TYR* 4.5 8.7 - - + -
68E LEU* 5.1 5.6 - - + -
100E TRP* 4.1 26.0 - - + -
101E TYR 3.4 10.5 - - - +
102E GLU* 2.8 27.1 + - + +
132E VAL* 3.2 5.2 - - - +
133E TRP* 2.8 57.2 + - + +
136E GLY 5.4 0.2 + - - -
167E ARG* 3.2 15.6 + - - +
168E ILE* 1.3 71.7 - - - +
170E ILE* 1.3 65.3 + - - +
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Residues in contact with ILE 170 (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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45E TRP* 3.9 25.4 - - + -
99E VAL 3.7 1.4 - - - +
100E TRP* 3.5 1.5 - - - -
101E TYR* 2.8 47.2 + - + +
123E ILE* 3.9 29.4 - - + -
130E ALA* 4.6 6.7 - - + -
131E ILE 3.3 9.2 - - - +
132E VAL* 4.1 15.0 - - + -
133E TRP* 4.6 1.1 - - - -
149E PHE* 5.7 2.0 - - + -
168E ILE* 4.0 13.5 - - + -
169E THR* 1.3 80.2 - - - +
171E ALA* 1.3 63.8 + - - +
172E ILE* 3.9 24.4 + - + -
214E LEU* 4.2 15.5 - - + -
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Residues in contact with ALA 171 (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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59E PHE* 4.3 0.7 - - + -
98E TRP* 3.5 22.8 - - + -
99E VAL 3.3 5.4 - - - +
100E TRP* 3.9 22.2 - - + +
130E ALA* 3.2 5.0 - - - +
131E ILE* 2.9 32.5 + - + -
133E TRP* 3.6 26.7 - - + -
170E ILE* 1.3 73.8 - - - +
172E ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 172 (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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97E GLY 3.5 1.7 - - - +
98E TRP* 3.2 4.4 - - - -
99E VAL* 2.9 44.5 + - + +
101E TYR* 4.1 12.8 - - + -
126E ALA* 4.3 11.0 - - + -
127E HIS* 3.6 33.0 - - + +
129E TYR 3.3 6.7 - - - +
130E ALA* 4.4 1.3 - - + -
170E ILE* 3.9 12.6 - - + +
171E ALA* 1.3 78.8 - - - +
173E ASN* 1.3 63.2 + - - +
174E ASN* 4.2 0.9 + - + +
212E ALA* 5.4 3.4 - - + -
213E GLY* 3.9 22.4 - - - +
214E LEU* 3.6 35.2 - - + -
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Residues in contact with ASN 173 (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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97E GLY 3.3 5.9 + - - -
98E TRP* 3.1 29.1 - - + +
127E HIS* 3.6 2.4 - - - +
128E SER* 3.2 23.4 + - - -
129E TYR* 2.8 17.4 + - + +
172E ILE* 1.3 73.4 - - - +
174E ASN* 1.3 59.5 + - - +
175E THR* 2.8 33.1 + - - -
1H NAG 1.4 73.0 + - - +
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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