Contacts of the strand formed by residues 98 - 105 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B ASP* 3.1 29.5 + - + +
55B ARG* 3.3 29.4 + - + +
56B ARG* 5.7 2.2 - - - +
59B PHE* 3.4 28.3 - + - -
95B PHE* 3.4 6.2 - - - -
97B GLY* 1.3 71.8 - - - -
99B VAL* 1.3 61.1 + - - +
100B TRP* 3.9 16.1 - - + +
129B TYR* 4.0 19.1 - + + -
131B ILE* 3.9 24.5 - - + -
171B ALA* 3.5 38.6 - - + -
172B ILE 3.3 6.1 - - - -
173B ASN* 3.1 49.0 - - + +
1F NAG 3.5 23.1 + - + -
6F MAN 5.5 2.0 + - - -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B PHE* 3.6 20.2 - - + -
48B ARG 3.6 4.7 - - - +
49B ALA* 4.0 5.2 - - + -
83B PHE* 3.7 27.1 - - + -
95B PHE* 3.4 30.7 - - + -
97B GLY 5.1 0.7 - - - +
98B TRP* 1.3 74.3 - - - +
100B TRP* 1.3 62.7 + - - +
101B TYR* 3.8 25.8 - - + -
170B ILE 3.7 0.7 - - - +
171B ALA* 3.2 4.7 - - - -
172B ILE* 2.9 51.3 + - + +
174B ASN* 5.9 0.4 - - - +
213B GLY* 5.3 0.4 - - - -
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Residues in contact with TRP 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER 3.7 0.2 - - - +
47B PHE* 3.1 8.8 - - - -
48B ARG* 2.8 40.3 + - + +
50B ASP* 4.1 6.3 + - + +
58B GLY* 3.7 34.4 - - - -
59B PHE* 3.9 21.3 - + - -
63B TRP* 3.6 32.0 - + + -
64B TYR* 4.0 24.7 - + + -
68B LEU* 3.8 21.4 - - + +
98B TRP* 3.9 22.0 - - - +
99B VAL* 1.3 80.4 - - - +
101B TYR* 1.3 63.2 + - - +
133B TRP* 3.6 33.7 - + - -
169B THR* 4.0 16.8 - - + -
170B ILE 3.4 3.6 - - - -
171B ALA* 4.0 11.7 - - + -
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TRP* 3.9 21.5 - - + -
46B SER 3.2 6.5 - - - -
47B PHE* 3.6 22.9 - + - -
68B LEU* 4.7 1.1 - - - -
77B MET* 3.6 30.5 - - + +
78B PRO 4.8 0.2 - - - -
79B VAL* 3.7 22.9 - - + -
81B SER 4.2 4.7 + - - -
83B PHE* 3.9 8.3 - - - +
99B VAL* 3.8 17.3 - - + -
100B TRP* 1.3 76.8 - - - +
102B GLU* 1.3 63.5 + - - +
169B THR* 3.4 4.3 - - - +
170B ILE* 2.8 38.8 + - + +
172B ILE* 4.2 9.2 - - + -
213B GLY* 3.3 20.9 - - - -
214B LEU* 3.4 37.5 + - + -
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TRP* 3.5 7.5 - - - -
46B SER* 2.8 46.4 + - - +
64B TYR* 5.4 0.3 - - - -
66B ARG 4.1 0.5 - - - +
67B PRO* 3.4 9.2 - - - +
68B LEU* 2.8 45.0 + - + +
69B TRP* 5.6 0.3 - - - -
101B TYR* 1.3 76.9 - - - +
103B ARG* 1.3 65.5 + - - +
104B GLU* 4.6 5.0 - - + +
167B ARG* 3.1 33.1 + - + -
168B ILE 3.2 12.8 - - - +
169B THR* 2.8 25.3 + - + +
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS* 5.5 3.2 - - - +
40B GLU 4.5 2.4 + - - -
41B LEU* 3.5 30.4 + - + +
42B ASP 3.1 28.9 + - - -
44B LEU 3.2 29.9 + - - +
45B TRP* 3.5 45.0 - - + +
102B GLU* 1.3 75.8 - - - +
104B GLU* 1.3 77.2 + - - +
105B VAL* 3.9 13.7 + - + +
166B LEU 3.6 1.4 - - - +
167B ARG* 3.6 1.0 - - - -
168B ILE* 2.9 33.7 + - + +
32E GLU* 5.9 0.8 + - - -
40E GLU* 5.7 2.4 + - - -
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B PRO* 4.2 14.4 - - - +
102B GLU* 4.6 5.5 - - + +
103B ARG* 1.3 88.4 + - - +
105B VAL* 1.3 62.2 + - - +
165B ARG* 3.5 37.8 + - - +
166B LEU 3.2 5.6 - - - +
167B ARG* 3.7 30.5 - - + -
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS* 3.3 28.5 - - - +
41B LEU* 3.8 23.8 - - + -
103B ARG* 3.9 12.6 - - + +
104B GLU* 1.3 79.7 - - - +
106B ILE* 1.3 70.9 + - - +
107B LEU* 3.9 15.6 + - + -
165B ARG* 3.4 5.3 - - - -
166B LEU* 2.7 55.5 + - + +
168B ILE* 4.1 19.1 - - + -
220B LEU* 4.3 2.5 - - + -
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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