Contacts of the strand formed by residues 94 - 101 (chain A) in PDB entry 3HD1
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 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.0 21.1 - - + -
8A GLY 3.4 13.2 - - - +
9A SER* 4.9 2.2 - - - -
17A GLN* 3.7 19.7 - - + +
18A VAL* 5.2 1.8 - - + -
21A ALA* 3.8 28.9 - - + -
76A ILE* 4.4 10.8 - - + +
77A GLU* 3.8 8.2 - - + +
80A GLN* 4.5 4.9 - - + +
81A GLY* 3.5 31.4 + - - +
92A ARG* 3.0 27.7 + - - +
93A THR* 1.3 80.0 - - - +
95A ASP* 1.3 61.1 + - - +
96A LEU* 4.3 22.2 - - + -
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Residues in contact with ASP 95 (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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6A ALA 3.3 5.7 - - - +
7A ILE* 3.5 2.1 - - - -
8A GLY* 2.8 45.0 + - - +
53A TYR* 6.5 1.3 - - + -
77A GLU* 3.6 0.2 - - - +
92A ARG* 2.9 20.6 + - - +
93A THR 5.7 0.2 - - - -
94A LEU* 1.3 73.8 - - - +
96A LEU* 1.3 63.5 + - - +
97A ASP* 3.1 7.7 - - - +
161A MG 2.2 27.6 - - - -
162A MG 2.2 28.2 - - - -
171A APC 2.9 6.1 + - - -
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Residues in contact with LEU 96 (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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5A ILE* 4.4 10.3 - - + -
6A ALA 3.4 2.5 - - - +
7A ILE* 3.7 35.2 - - + -
21A ALA* 4.8 2.5 - - + -
25A LEU* 4.3 16.8 - - + -
70A LEU* 5.4 0.2 - - - +
73A THR* 3.6 45.3 + - - +
76A ILE* 3.8 27.4 - - + -
77A GLU* 2.8 24.3 + - + +
94A LEU* 4.3 14.4 - - + -
95A ASP* 1.3 76.8 - - - +
97A ASP* 1.3 64.4 + - - +
98A ILE 4.3 0.3 + - - -
161A MG 4.2 0.3 - - - -
171A APC 4.1 8.1 - - - -
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Residues in contact with ASP 97 (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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5A ILE* 3.3 5.0 - - - +
6A ALA* 2.8 39.5 + - + +
95A ASP* 3.1 7.2 - - - +
96A LEU* 1.3 74.3 - - - +
98A ILE* 1.3 64.4 + - - +
99A MET 3.3 0.9 + - - -
115A HIS* 3.3 24.3 + - + -
124A MET* 4.1 14.4 - - + +
161A MG 2.2 27.8 - - - -
162A MG 2.2 28.0 - - - -
171A APC 3.1 18.0 + - - +
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Residues in contact with ILE 98 (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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3A ALA* 5.2 1.1 - - + -
4A TYR 3.8 4.7 - - - +
5A ILE* 4.6 8.3 - - + +
66A PRO 4.2 8.1 - - - +
69A LEU* 4.1 22.2 - - + -
70A LEU* 4.0 36.3 - - + +
73A THR* 4.7 9.2 - - + +
96A LEU 5.5 0.2 - - - +
97A ASP* 1.3 71.4 - - - +
99A MET* 1.3 62.6 + - - +
100A LEU 3.7 19.5 - - - +
101A PHE* 4.5 12.3 - - + -
111A LEU* 4.2 12.1 - - + -
113A VAL* 4.0 16.7 - - + +
115A HIS* 3.8 6.7 + - - +
171A APC 2.8 39.1 + - + +
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Residues in contact with MET 99 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A TYR* 2.7 18.5 + - + +
5A ILE 3.9 8.7 - - - +
6A ALA* 3.8 41.7 - - + +
57A ALA* 4.1 18.8 - - + -
98A ILE* 1.3 73.7 - - - +
100A LEU* 1.3 63.2 + - + +
113A VAL* 3.8 1.1 - - - +
114A PRO* 3.2 10.0 - - - +
115A HIS* 3.0 27.6 + - + -
118A MET* 3.7 28.9 - - + +
124A MET* 3.9 37.9 - - + +
128A LEU* 4.2 18.2 - - + -
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Residues in contact with LEU 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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2A VAL 4.7 0.2 - - - -
3A ALA* 3.4 2.3 - - - -
4A TYR* 2.9 42.6 + - + +
98A ILE* 3.7 7.0 - - - +
99A MET* 1.3 88.5 - - + +
101A PHE* 1.3 62.1 + - - +
102A GLY 4.0 10.5 - - - +
113A VAL* 3.8 5.6 - - + -
114A PRO* 3.7 28.3 - - + -
118A MET* 4.7 0.2 - - + -
128A LEU* 4.3 9.2 - - + -
135A LEU* 3.2 43.3 - - + -
136A VAL 5.4 1.8 - - - +
137A PHE* 3.8 21.3 - - + -
138A PRO* 4.2 12.3 - - + -
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Residues in contact with PHE 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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1A THR* 3.9 17.3 - - + -
2A VAL 4.1 1.3 - - - -
3A ALA* 3.9 13.5 - - + -
62A THR* 3.9 24.0 - - + -
64A LEU 3.3 24.9 - - - -
65A ALA 4.5 0.4 - - - -
66A PRO* 3.6 44.0 - - + -
69A LEU* 4.0 13.9 - - + -
98A ILE* 4.5 8.7 - - + -
100A LEU* 1.3 74.3 - - - +
102A GLY* 1.3 66.6 + - - +
104A GLU* 3.0 44.8 + - + +
106A ILE* 4.3 8.1 - - + -
113A VAL* 3.6 18.1 - - + +
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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