Contacts of the strand formed by residues 95 - 101 (chain D) in PDB entry 2W93
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 VAL 95 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D ALA 5.2 2.2 - - - +
58D ALA* 3.8 15.7 - - + -
59D ASP* 3.9 18.4 - - - +
68D SER* 3.4 22.2 - - - +
70D ILE* 3.8 20.4 - - + +
85D ILE* 4.2 11.7 - - + -
88D SER* 3.5 30.5 - - - +
93D VAL* 3.0 11.1 + - + +
94D GLY* 1.3 73.5 - - - -
96D LEU* 1.3 62.9 + - - +
97D HIS 3.5 1.4 + - - -
156D THR* 3.5 3.9 - - - +
162D PRO* 3.0 27.4 - - + +
163D VAL 3.1 4.2 + - - -
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Residues in contact with LEU 96 (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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10D LEU* 4.5 8.5 - - + -
14D LEU* 4.3 15.3 - - + -
67D MET* 4.4 5.6 - - + -
68D SER 2.9 17.8 + - - +
69D CYS* 3.2 7.6 - - - -
70D ILE 2.9 27.5 + - - +
95D VAL* 1.3 70.3 - - - +
97D HIS* 1.3 59.1 + - - +
98D VAL* 3.9 20.9 - - + -
152D CYS* 3.9 26.5 - - + +
153D ILE* 3.9 25.6 - - + -
156D THR* 3.7 18.6 - - - +
163D VAL* 3.7 15.7 - - + +
165D LEU* 4.0 15.7 - - + -
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Residues in contact with HIS 97 (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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70D ILE* 3.4 25.4 - - + -
72D THR* 2.8 34.0 + - + +
78D GLU* 3.8 29.8 - - + -
81D ALA* 4.1 9.6 - - + +
82D LEU* 4.4 7.1 - - + +
85D ILE* 3.8 30.2 - - + +
95D VAL 3.5 1.8 + - - +
96D LEU* 1.3 71.3 - - - +
98D VAL* 1.3 63.8 + - - +
99D VAL* 3.7 8.8 + - + +
129D SER* 4.7 0.4 + - - -
162D PRO* 5.9 0.4 - - + -
163D VAL 2.9 14.9 + - - +
164D TYR* 3.5 16.0 - + + +
165D LEU 2.8 29.8 + - - -
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Residues in contact with VAL 98 (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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10D LEU* 4.2 9.9 - - + -
33D LEU* 4.0 17.3 - - + -
69D CYS* 3.8 21.3 - - - -
70D ILE 2.8 6.3 + - - +
71D ILE* 3.1 16.5 - - + +
72D THR 2.9 24.6 + - - -
96D LEU* 3.9 19.3 - - + -
97D HIS* 1.3 76.9 - - - +
99D VAL* 1.3 62.9 + - - +
100D GLY 4.2 0.2 - - - -
165D LEU* 3.2 19.1 - - + +
167D LEU* 3.7 30.5 - - + -
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Residues in contact with VAL 99 (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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72D THR* 3.5 5.6 - - - +
73D THR 3.9 4.9 - - - -
74D PHE* 3.7 19.3 - - - +
78D GLU* 3.6 27.1 - - + +
97D HIS* 3.7 22.2 - - + +
98D VAL* 1.3 80.6 - - - +
100D GLY* 1.3 62.7 + - - +
101D VAL* 3.4 9.5 + - + +
164D TYR* 3.6 37.5 - - + +
165D LEU 2.9 9.2 + - - +
166D GLY* 3.5 2.2 - - - -
167D LEU* 2.8 31.7 + - - +
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Residues in contact with GLY 100 (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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29D PHE* 3.2 30.3 - - - +
30D ASN* 4.0 10.3 - - - +
33D LEU* 5.4 3.8 - - - -
71D ILE* 4.8 1.4 - - - +
72D THR 3.0 11.3 + - - -
73D THR* 4.0 0.2 - - - -
74D PHE* 3.0 27.7 + - - +
98D VAL* 4.2 0.6 - - - +
99D VAL* 1.3 69.8 - - - +
101D VAL* 1.3 57.7 + - - -
167D LEU* 3.6 8.5 - - - -
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Residues in contact with VAL 101 (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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29D PHE* 4.2 5.4 - - - +
74D PHE* 3.8 18.4 - - + -
99D VAL* 3.6 21.8 - - + +
100D GLY* 1.3 79.1 - - - +
102D PRO* 1.3 79.0 - - + +
107D GLN* 4.0 5.8 - - - +
138D MET* 3.8 31.0 - - + -
164D TYR* 4.8 1.6 - - - +
166D GLY* 4.5 0.2 - - - -
167D LEU 2.9 11.1 + - - +
168D PRO* 3.3 34.3 - - + +
169D ALA* 2.9 24.3 + - - +
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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