Contacts of the strand formed by residues 98 - 105 (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 TRP 98 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50E ASP* 3.0 29.2 + - + +
55E ARG* 3.2 28.4 + - + +
56E ARG* 5.2 3.0 - - - +
59E PHE* 3.5 28.1 - + - -
95E PHE* 3.4 9.0 - - - -
97E GLY* 1.3 71.7 - - - -
99E VAL* 1.3 58.4 + - - +
100E TRP* 3.8 16.4 - - - +
129E TYR* 4.1 17.0 - + - -
131E ILE* 3.9 23.6 - - + -
171E ALA* 3.5 39.5 - - + -
172E ILE* 3.2 18.8 - - - -
173E ASN* 3.1 37.0 - - + +
661E BMA 5.7 1.0 + - - -
1H NAG 3.5 21.8 + - + -
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Residues in contact with VAL 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E PHE* 3.6 26.7 - - + -
48E ARG 3.6 3.6 - - - +
49E ALA* 4.1 6.5 - - + -
83E PHE* 3.7 29.8 - - + -
95E PHE* 3.8 19.1 - - + -
97E GLY 4.1 0.4 + - - +
98E TRP* 1.3 76.3 - - - +
100E TRP* 1.3 62.0 + - - +
101E TYR* 3.8 24.0 - - + -
170E ILE 3.7 1.6 - - - +
171E ALA* 3.3 3.5 - - - -
172E ILE* 2.9 50.2 + - + +
174E ASN* 6.4 0.2 - - - -
213E GLY* 5.4 0.2 - - - -
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Residues in contact with TRP 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E SER 3.8 0.2 - - - +
47E PHE* 3.2 7.8 - - - -
48E ARG 2.8 40.3 + - - +
50E ASP* 4.1 6.5 + - + +
58E GLY* 3.7 29.3 - - - -
59E PHE* 3.6 26.2 - + - -
63E TRP* 3.5 36.8 - + + -
64E TYR* 4.0 24.5 - + + -
68E LEU* 3.9 19.9 - - + +
98E TRP* 3.8 20.8 - - - +
99E VAL* 1.3 80.3 - - - +
101E TYR* 1.3 62.6 + - - +
133E TRP* 3.6 33.4 - + - -
169E THR* 4.1 15.7 - - + -
170E ILE 3.5 3.6 - - - -
171E ALA* 3.9 11.4 - - + -
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Residues in contact with TYR 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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45E TRP* 3.9 28.9 - - + -
46E SER 3.3 5.8 - - - -
47E PHE* 3.7 25.2 - + - -
68E LEU* 4.5 1.8 - - - -
77E MET* 3.6 30.0 - - + +
79E VAL* 3.8 16.2 - - + -
81E SER 4.4 3.3 + - - -
83E PHE* 3.9 5.0 - - - +
99E VAL* 3.8 15.7 - - + -
100E TRP* 1.3 77.7 - - - +
102E GLU* 1.3 63.7 + - - +
169E THR* 3.4 5.7 - - - +
170E ILE* 2.8 37.9 + - + +
172E ILE* 4.1 20.9 - - + -
213E GLY* 3.3 20.2 - - - -
214E LEU* 3.4 27.9 + - + -
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Residues in contact with GLU 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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45E TRP* 3.5 7.8 - - - -
46E SER* 2.9 43.3 + - - +
63E TRP 5.4 0.3 - - - +
66E ARG 4.1 0.7 - - - +
67E PRO* 3.4 8.0 - - - +
68E LEU* 2.8 45.5 + - + +
69E TRP* 5.6 0.7 - - - -
101E TYR* 1.3 77.1 - - - +
103E ARG* 1.3 65.5 + - - +
104E GLU* 4.5 4.7 - - + +
167E ARG* 2.9 34.6 + - + -
168E ILE 3.2 12.8 - - - +
169E THR* 2.8 24.7 + - - +
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Residues in contact with ARG 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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40B GLU* 5.5 2.6 + - - -
40E GLU 4.5 2.8 + - - -
41E LEU* 3.0 44.8 + - + +
42E ASP 3.2 24.5 + - - -
43E GLY 3.9 2.4 - - - -
44E LEU 3.2 28.7 + - - +
45E TRP* 3.3 37.3 - - + +
102E GLU* 1.3 75.1 - - - +
104E GLU* 1.3 78.3 + - - +
105E VAL* 3.9 13.2 - - + +
166E LEU 3.7 0.5 - - - +
167E ARG* 3.6 1.4 - - - -
168E ILE* 2.9 34.5 + - + +
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Residues in contact with GLU 104 (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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67E PRO* 4.2 15.5 - - - +
69E TRP* 5.1 5.0 + - - -
102E GLU* 4.5 4.7 - - + +
103E ARG* 1.3 90.0 + - - +
105E VAL* 1.3 63.2 + - - +
165E ARG* 4.8 16.1 - - + +
166E LEU 3.2 4.5 - - - +
167E ARG* 3.9 33.8 - - + -
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Residues in contact with VAL 105 (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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32B GLU* 6.2 0.4 - - - -
39E LYS* 4.2 12.3 - - - -
41E LEU* 3.8 34.1 - - + -
103E ARG* 3.9 12.1 - - + +
104E GLU* 1.3 79.2 - - - +
106E ILE* 1.3 75.0 + - - +
107E LEU* 3.8 16.9 + - + -
165E ARG* 3.4 5.0 - - - -
166E LEU* 2.7 47.4 + - + +
168E ILE* 4.0 19.7 - - + -
220E LEU* 4.2 3.6 - - + -
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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