Contacts of the strand formed by residues 19 - 25 (chain D) in PDB entry 2P5W
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 19 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.3 14.4 - - + -
13D VAL* 3.8 33.9 - - + -
17D GLU* 3.8 15.7 - - + +
18D ASN* 1.3 78.0 - - - +
20D VAL* 1.3 62.3 + - - +
21D LEU* 4.2 4.3 - - + -
76D TYR* 3.4 1.9 - - - -
77D ILE* 2.7 50.2 + - + +
80D SER* 4.0 15.7 - - - -
110D LEU* 3.5 42.4 - - + -
112D VAL* 4.5 0.2 - - + -
1004D GOL 3.1 8.8 + - - -
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PRO* 4.4 8.7 - - - +
11D LEU* 4.9 2.9 - - - +
18D ASN 5.3 1.8 - - - +
19D LEU* 1.3 76.4 - - - +
21D LEU* 1.3 66.5 + - - +
22D ASN* 4.3 10.0 + - - +
74D THR* 4.4 11.2 - - + -
75D LEU 3.5 5.2 - - - -
76D TYR* 3.8 17.5 - - + -
1004D GOL 3.6 15.3 - - - +
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE 4.1 3.4 - - - +
8D PRO* 4.5 2.9 - - + -
11D LEU* 3.2 35.0 - - + -
19D LEU* 4.8 7.9 - - + -
20D VAL* 1.3 75.8 - - - +
22D ASN* 1.3 61.3 + - - +
35D TRP* 4.2 11.9 - - + -
74D THR* 3.5 3.8 - - - +
75D LEU* 2.8 48.3 + - + +
77D ILE* 4.7 11.4 - - + -
88D TYR* 3.7 39.3 - - + -
108D THR* 3.9 28.9 - - + +
110D LEU* 5.3 2.9 - - + -
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Residues in contact with ASN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D GLN* 3.2 8.8 - - - +
7D ILE* 2.9 58.9 + - + +
20D VAL* 4.7 10.4 - - - +
21D LEU* 1.3 74.9 - - - +
23D CYS* 1.3 61.4 + - - +
24D SER* 4.2 2.2 - - - +
35D TRP* 4.2 3.5 - - - -
67D ASP* 5.1 0.2 + - - -
72D SER* 4.6 7.2 + - - +
73D SER 3.6 4.2 + - - -
74D THR* 3.1 35.1 + - - +
108D THR* 5.0 1.2 + - - -
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Residues in contact with CYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.5 13.2 - - - -
5D THR 3.5 3.1 - - - -
6D GLN* 4.3 0.2 - - - -
22D ASN* 1.3 73.3 - - - +
24D SER* 1.3 61.1 + - - +
25D PHE* 4.1 3.4 - - - -
33D LEU* 4.3 15.7 - - - -
35D TRP* 3.4 23.3 - - + -
72D SER* 3.5 2.2 - - - -
73D SER* 2.9 40.3 + - - +
90D CYS* 2.0 47.6 - - - -
92D VAL* 5.3 1.3 - - - -
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Residues in contact with SER 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN 3.8 0.6 - - - +
4D VAL* 3.4 5.0 - - - +
5D THR* 2.7 61.9 + - - +
7D ILE* 6.1 1.0 - - - +
22D ASN* 4.2 2.6 - - - -
23D CYS* 1.3 74.2 - - - +
25D PHE* 1.3 61.2 + - - +
71D GLY 3.4 11.7 - - - -
72D SER* 4.3 8.5 - - - +
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Residues in contact with PHE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D GLN* 3.6 14.8 - - - +
3D GLN 3.4 7.4 - - - +
4D VAL* 4.2 10.8 - - + -
23D CYS* 4.1 4.7 - - - -
24D SER* 1.3 77.8 - - - +
26D THR* 1.3 63.3 + - - +
27D ASP 3.5 18.1 - - - -
28D SER* 4.0 7.6 + - - -
30D ILE* 3.5 32.5 - - + -
33D LEU* 3.5 28.9 - - + -
66D LEU* 3.9 9.6 - - + -
70D SER 3.3 26.2 - - - -
71D GLY* 3.0 25.0 + - - +
72D SER* 3.6 19.7 - - - -
92D VAL* 4.2 6.7 - - + -
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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