Contacts of the strand formed by residues 98 - 105 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ASP* 3.0 29.1 + - + +
55A ARG* 3.3 29.5 + - + +
56A ARG* 5.3 5.2 - - + +
59A PHE* 3.4 30.5 - + + -
95A PHE* 3.3 10.4 - - - -
97A GLY* 1.3 71.7 - - - -
99A VAL* 1.3 59.5 + - - +
100A TRP* 3.8 15.9 - - - +
129A TYR* 4.0 17.9 - + - -
131A ILE* 3.9 22.9 - - + -
171A ALA* 3.6 31.4 - - + -
172A ILE 3.4 8.7 - - - -
173A ASN* 3.1 52.0 - - + +
1C NAG 3.5 22.5 + - + -
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PHE* 3.8 21.5 - - + -
48A ARG 3.7 3.6 - - - -
49A ALA* 4.1 6.3 - - + -
83A PHE* 3.7 34.1 - - + -
95A PHE* 3.6 26.2 - - + -
97A GLY 5.3 0.2 - - - +
98A TRP* 1.3 71.8 - - - +
100A TRP* 1.3 63.8 + - - +
101A TYR* 4.0 16.3 - - + -
170A ILE 3.8 1.0 - - - +
171A ALA* 3.2 4.0 - - - -
172A ILE* 2.9 56.2 + - + +
174A ASN* 6.2 0.9 - - + -
213A GLY* 5.4 0.4 - - - -
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Residues in contact with TRP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PHE* 3.2 8.7 - - - -
48A ARG 2.8 42.8 + - - +
50A ASP* 4.0 7.0 + - + +
58A GLY* 3.7 34.1 - - - -
59A PHE* 3.7 22.2 - + - -
63A TRP* 3.8 33.2 - + + -
64A TYR* 4.0 25.4 - + + -
68A LEU* 3.7 20.2 - - + +
98A TRP* 3.8 20.2 - - - +
99A VAL* 1.3 84.0 - - - +
101A TYR* 1.3 61.5 + - - +
133A TRP* 3.7 31.4 - + - -
169A THR* 4.1 15.5 - - + -
170A ILE 3.5 3.6 - - - -
171A ALA* 4.0 12.1 - - + -
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Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 3.8 28.0 - - + -
46A SER 3.3 5.6 - - - -
47A PHE* 3.6 25.7 - + - -
68A LEU* 4.4 1.3 - - - -
77A MET* 3.7 29.6 - - + +
78A PRO 5.0 0.2 + - - -
79A VAL* 3.8 16.2 - - + -
81A SER 4.3 4.3 + - - -
83A PHE* 3.9 5.0 - - - +
99A VAL* 4.0 10.5 - - + -
100A TRP* 1.3 77.7 - - - +
102A GLU* 1.3 64.1 + - - +
168A ILE 4.0 0.2 - - - +
169A THR* 3.3 5.2 - - - +
170A ILE* 2.8 38.5 + - + +
172A ILE* 3.8 30.5 - - + -
213A GLY* 3.3 19.5 - - - -
214A LEU* 3.4 24.3 + - + -
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 3.5 8.1 - - - -
46A SER* 2.9 43.7 + - - +
63A TRP 5.4 0.3 - - - +
66A ARG 4.0 0.7 - - - +
67A PRO* 3.3 8.7 - - - +
68A LEU* 2.8 45.0 + - + +
69A TRP* 5.7 0.3 - - - -
101A TYR* 1.3 78.1 - - - +
103A ARG* 1.3 64.6 + - - +
104A GLU* 5.2 4.3 - - + +
167A ARG* 2.9 34.7 + - + -
168A ILE 3.2 13.5 - - - +
169A THR* 2.7 25.1 + - + +
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLU 4.8 2.2 + - - -
41A LEU* 3.6 28.9 + - + +
42A ASP 3.0 34.9 + - - -
43A GLY* 3.7 1.0 - - - -
44A LEU 3.1 30.6 + - - +
45A TRP* 3.6 37.5 - - + +
102A GLU* 1.3 75.1 - - - +
104A GLU* 1.3 77.6 + - - +
105A VAL* 4.1 11.5 + - + +
166A LEU 3.7 0.9 - - - +
167A ARG* 3.5 1.6 - - - -
168A ILE* 2.9 34.3 + - + +
32D GLU* 5.7 2.6 + - - -
40D GLU* 5.7 2.8 + - - -
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PRO* 4.5 11.3 - - - +
102A GLU* 5.2 3.8 - - + +
103A ARG* 1.3 87.9 + - - +
105A VAL* 1.3 62.0 + - - +
106A ILE 4.4 0.2 - - - -
165A ARG* 3.5 45.1 + - + +
166A LEU 3.2 4.3 - - - +
167A ARG* 3.6 33.3 - - + +
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS* 4.2 10.8 - - - -
41A LEU* 3.7 31.9 - - + -
103A ARG* 4.1 9.6 - - + +
104A GLU* 1.3 79.6 - - - +
106A ILE* 1.3 67.5 + - - +
107A LEU* 3.5 25.5 + - + -
165A ARG* 3.1 5.5 - - - -
166A LEU* 2.6 52.9 + - + +
168A ILE* 4.0 21.5 - - + -
220A LEU* 4.1 3.1 - - + -
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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