Contacts of the strand formed by residues 88 - 93 (chain A) in PDB entry 1V1A
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 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.0 3.1 - - - +
12A VAL* 3.2 23.3 - - + +
14A LEU* 3.7 14.4 - - + -
61A LEU* 4.2 9.9 - - + -
87A GLY* 1.3 75.5 - - - +
89A TYR* 1.3 65.6 + - - +
90A LEU* 3.3 28.5 - - + -
103A TYR* 4.1 0.2 - - - -
104A TYR* 2.9 49.2 + - + +
105A ARG* 4.8 0.9 - - - +
88B LEU* 4.3 5.4 - - + -
90B LEU* 4.0 17.3 - - + -
104B TYR* 3.7 35.2 - - + +
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Residues in contact with TYR 89 (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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11A LEU* 3.8 19.5 - - + -
12A VAL 2.8 13.8 + - - +
13A ALA* 3.4 23.2 - - + -
14A LEU* 2.9 24.1 + - - +
33A GLY* 5.3 0.2 - - - -
88A LEU* 1.3 78.3 - - - +
90A LEU* 1.3 73.9 + - - +
91A ARG* 3.1 30.7 + - + -
101A VAL* 3.6 18.8 - - + -
102A PHE 3.3 12.1 - - - +
103A TYR* 3.8 23.3 - + + -
247A VAL* 3.5 3.4 - - + +
287A ASP* 2.7 23.2 + - - -
1302A KDG 3.3 30.9 - - + -
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Residues in contact with LEU 90 (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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14A LEU* 3.5 26.5 - - + +
22A LEU* 4.0 28.0 - - + -
28A LEU* 4.6 12.6 - - + -
88A LEU* 3.3 28.9 - - + -
89A TYR* 1.3 76.8 - - - +
91A ARG* 1.3 63.2 + - - +
101A VAL* 3.6 9.0 - - - +
102A PHE* 2.9 34.9 + - + +
104A TYR* 3.9 18.6 - - + -
14B LEU* 5.7 1.1 - - + -
61B LEU* 4.3 27.6 - - + -
88B LEU* 4.2 5.6 - - + -
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Residues in contact with ARG 91 (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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13A ALA* 4.0 2.0 - - - +
14A LEU 3.1 14.3 + - - +
15A VAL* 3.3 33.8 - - + +
16A PRO* 2.9 32.7 - - - +
22A LEU* 4.4 5.9 - - - +
89A TYR* 3.1 20.7 + - + -
90A LEU* 1.3 77.9 - - - +
92A GLU* 1.3 65.1 + - - +
93A TYR* 4.2 4.0 - - + -
100A ARG 3.9 2.7 - - - -
101A VAL* 4.3 12.6 - - + -
245A ASP* 2.5 37.1 + - - +
247A VAL* 2.9 38.6 - - + +
286A GLY* 3.2 12.5 + - - +
287A ASP* 2.6 25.1 + - - -
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Residues in contact with GLU 92 (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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16A PRO* 4.9 3.1 - - - -
20A GLY 3.6 13.0 - - - +
21A HIS* 3.3 9.1 - - - -
22A LEU* 3.2 20.1 + - + +
91A ARG* 1.3 77.0 - - - +
93A TYR* 1.3 60.7 + - - +
94A LEU* 3.2 29.0 - - + +
99A GLY* 2.9 4.3 - - - -
100A ARG* 2.8 60.8 + - - +
102A PHE* 4.3 5.8 - - + -
60B GLU* 2.8 40.2 - - - +
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Residues in contact with TYR 93 (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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15A VAL* 3.5 20.5 - - + +
16A PRO* 2.7 40.2 + - + +
17A GLN 3.3 15.9 + - - -
18A GLU 3.6 9.9 - - - -
19A PRO* 3.1 50.8 - - + +
20A GLY 3.1 23.3 + - - -
29A GLU* 5.4 0.7 + - - -
91A ARG* 4.4 5.6 - - + -
92A GLU* 1.3 75.0 - - - +
94A LEU* 1.3 62.5 + - - +
97A GLY 4.2 6.7 - - - +
99A GLY* 4.1 4.3 - - - -
244A VAL 5.1 12.3 - - - -
245A ASP* 5.0 15.5 - - + +
285A ARG* 5.5 3.8 - - - +
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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