Contacts of the strand formed by residues 5 - 11 (chain A) in PDB entry 1ESD
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 PRO 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ASP* 1.3 101.5 - - + +
6A VAL* 1.3 60.2 + - - +
7A PRO* 3.6 10.5 - - + +
55A THR* 3.2 17.0 - - + +
57A ASP* 3.5 31.4 - - + +
97A GLN* 4.3 5.2 + - - +
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Residues in contact with VAL 6 (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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4A ASP 4.1 5.2 - - - +
5A PRO* 1.3 73.4 - - - +
7A PRO* 1.3 71.8 - - - +
8A THR* 3.2 4.7 + - - -
54A ILE* 4.7 4.3 - - + -
55A THR 2.8 19.3 + - - +
56A LEU* 3.8 13.2 - - + -
57A ASP 3.1 15.1 + - - +
97A GLN* 4.0 20.4 - - + +
98A LEU* 3.9 37.0 - - + -
304A LEU* 4.5 20.4 - - + -
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Residues in contact with PRO 7 (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 PRO* 3.6 7.8 - - + +
6A VAL* 1.3 85.4 - - - +
8A THR* 1.3 56.1 + - - +
57A ASP* 3.4 22.0 - - - +
59A GLN* 3.5 30.1 - - + +
95A ASP* 3.6 27.8 - - + +
96A THR* 4.2 0.6 - - - -
97A GLN* 3.3 44.0 + - - +
98A LEU 3.4 7.4 + - - -
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Residues in contact with THR 8 (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 VAL 3.2 13.7 + - - -
7A PRO* 1.3 69.8 + - - +
9A VAL* 1.3 72.1 + - - +
10A PHE* 3.6 34.5 - - + -
56A LEU* 3.7 9.7 - - + +
57A ASP 3.0 8.1 + - - -
58A VAL* 3.5 15.5 - - - +
59A GLN* 2.8 29.0 + - - +
60A ALA 3.7 1.6 + - - +
96A THR* 4.8 0.4 - - - -
98A LEU* 3.3 37.5 - - + +
100A VAL* 4.8 2.5 - - + -
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Residues in contact with VAL 9 (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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8A THR* 1.3 80.6 - - - +
10A PHE* 1.3 74.8 + - - +
11A PHE* 4.6 6.2 - - + +
59A GLN* 3.8 21.8 - - + +
60A ALA* 3.6 9.0 - - + +
62A VAL* 4.9 2.0 - - + -
72A PHE* 6.3 0.2 - - + -
88A GLN 5.3 0.9 - - - +
91A ALA* 3.4 45.5 - - + +
92A LEU* 3.9 21.8 - - + -
96A THR* 3.9 11.6 - - + +
98A LEU 3.0 8.0 + - - +
99A THR* 3.4 6.8 - - + -
100A VAL 3.2 22.0 + - - +
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Residues in contact with PHE 10 (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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8A THR* 3.6 18.6 - - + -
9A VAL* 1.3 74.8 - - - +
11A PHE* 1.3 59.6 + - - +
16A THR* 5.0 0.2 - - + -
41A TYR* 5.1 2.0 - + - -
42A PRO* 3.4 41.7 - - + -
45A ALA* 5.5 3.6 - - + -
46A THR* 3.8 17.5 - - - -
56A LEU* 4.2 9.6 - - + -
58A VAL* 3.6 40.8 - - + -
60A ALA 3.2 6.0 + - - -
61A ASP* 3.4 26.5 - - + +
62A VAL* 2.9 27.2 + - - +
100A VAL* 3.3 39.3 - - + +
296A VAL* 5.3 2.9 - - + -
300A ILE* 5.1 5.6 - - + -
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Residues in contact with PHE 11 (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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9A VAL* 4.6 6.7 - - + -
10A PHE* 1.3 75.1 - - - +
12A GLY* 1.3 62.8 + - - +
16A THR* 3.2 10.6 - - - +
62A VAL* 4.2 5.8 - - + -
63A SER* 4.0 11.0 - - - +
72A PHE* 4.0 21.1 - + + -
88A GLN* 3.4 12.8 - - - +
99A THR* 3.9 29.6 - - + -
100A VAL 3.1 21.9 + - - -
101A GLY* 3.0 43.1 - - - -
103A LEU* 3.8 28.7 - - + -
168A LEU* 4.1 15.9 - - + -
169A LEU* 6.3 0.7 - - + -
172A ILE* 3.9 17.9 - - + -
182A VAL 4.4 4.9 - - - -
183A LEU* 5.0 4.0 - - + -
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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