Contacts of the strand formed by residues 81 - 91 (chain A) in PDB entry 1VAV
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 ASN 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A TRP* 3.3 38.5 - - + +
75A ARG 4.9 1.2 - - - +
76A TYR* 3.3 12.8 + - - +
78A ARG* 5.9 0.3 - - - +
79A ALA* 2.9 28.9 + - - +
80A ASP* 1.3 72.1 - - - +
82A TRP* 1.3 64.3 + - - +
163A GLY* 3.0 5.0 - - - -
164A VAL* 2.9 58.2 + - + +
194A PHE* 4.0 2.5 - - - -
221A SER 3.4 4.3 - - - -
222A HIS* 2.6 29.3 + - + +
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Residues in contact with TRP 82 (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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80A ASP* 4.3 23.9 - - + +
81A ASN* 1.3 80.7 + - - +
83A LEU* 1.3 59.9 + - - +
84A GLU* 4.0 16.3 - - + +
161A ARG* 3.4 56.3 - - + -
162A ILE 3.6 19.1 - - - -
163A GLY* 3.7 16.4 - - - -
164A VAL 5.4 1.7 - - - -
165A SER* 5.9 5.1 - - - +
171A SER* 3.7 28.3 - - - -
173A SER* 5.8 0.2 - - - -
194A PHE* 3.6 9.1 - - - -
219A ARG 3.9 0.2 - - - +
220A VAL* 3.3 4.3 - - - -
221A SER* 2.9 51.6 + - - +
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Residues in contact with LEU 83 (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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7A TRP* 4.4 2.2 - - + -
82A TRP* 1.3 72.9 - - - +
84A GLU* 1.3 76.5 + - - +
85A ALA* 5.1 0.9 - - + -
102A GLN 4.6 0.7 - - - +
160A TYR* 3.8 27.5 - - + +
161A ARG* 3.3 5.2 - - - +
162A ILE* 2.8 43.0 + - + +
194A PHE* 3.5 41.1 - - + -
195A LYS 3.8 21.8 - - - +
196A ALA* 4.5 3.6 - - + -
218A LEU* 3.7 24.9 - - + -
219A ARG 3.5 9.6 - - - +
220A VAL* 3.9 6.7 - - + +
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Residues in contact with GLU 84 (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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82A TRP* 4.0 17.9 - - + +
83A LEU* 1.3 85.6 - - - +
85A ALA* 1.3 62.6 + - - +
160A TYR* 3.6 4.3 - - - -
161A ARG* 4.0 32.6 + - + -
217A GLU* 4.2 5.0 - - - +
218A LEU* 3.3 4.0 + - - -
219A ARG* 2.6 88.6 + - + +
221A SER* 4.8 4.6 + - - -
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Residues in contact with ALA 85 (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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83A LEU* 5.1 1.8 - - + -
84A GLU* 1.3 76.4 - - - +
86A THR* 1.3 63.7 + - - +
87A LEU* 4.8 1.1 - - - -
159A SER* 3.1 7.3 - - - -
160A TYR* 2.9 63.1 + - + +
215A PHE* 3.8 16.4 - - + -
217A GLU* 3.2 17.6 + - - +
218A LEU* 4.6 4.7 - - + -
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Residues in contact with THR 86 (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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85A ALA* 1.3 72.8 + - - +
87A LEU* 1.3 63.7 + - - +
157A PRO* 4.7 8.7 - - + -
158A PHE 3.4 11.2 - - - +
159A SER* 4.1 0.4 - - - +
215A PHE* 3.2 5.5 - - - +
216A SER* 2.8 44.2 + - - +
217A GLU* 2.7 38.2 + - - +
14B GLY* 3.3 10.5 - - - -
15B ARG 3.0 30.6 + - - +
18B ILE* 4.4 11.0 - - + -
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Residues in contact with LEU 87 (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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85A ALA 4.8 0.2 - - - -
86A THR* 1.3 80.5 - - - +
88A ARG* 1.3 59.9 + - - +
89A ILE* 3.9 18.4 - - + -
100A ILE* 4.3 11.0 - - + -
157A PRO* 3.0 6.0 - - - +
158A PHE* 2.7 86.4 + - + +
160A TYR* 3.6 24.7 - - + -
213A ALA* 4.6 3.4 - - + -
214A THR 3.2 14.4 - - - +
215A PHE* 3.7 35.0 - - + -
216A SER* 4.4 1.8 - - - +
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Residues in contact with ARG 88 (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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39A ASP* 2.8 42.3 + - - +
42A ARG* 4.2 11.9 - - - +
87A LEU* 1.3 75.7 - - - +
89A ILE* 1.3 62.0 + - - +
90A GLU* 2.9 33.5 + - + +
155A GLY* 3.6 31.4 - - - +
156A GLN 3.9 6.1 - - - -
157A PRO* 4.1 10.5 - - + -
158A PHE* 4.4 1.3 - - - -
213A ALA* 3.4 5.4 - - - +
214A THR* 3.1 40.0 + - - +
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Residues in contact with ILE 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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87A LEU* 3.9 25.6 - - + -
88A ARG* 1.3 73.0 - - - +
90A GLU* 1.3 61.6 + - - +
91A ALA 3.8 2.5 - - - +
92A VAL* 3.6 20.6 - - + -
98A MET* 3.6 34.8 - - + -
100A ILE* 4.2 7.0 - - + -
121A TYR* 3.6 42.2 - - + +
153A PRO 5.4 0.8 + - - +
154A LEU* 3.4 16.5 - - + +
155A GLY 2.8 29.7 + - - +
156A GLN 4.7 1.4 + - - -
158A PHE* 3.8 10.8 - - + -
212A ARG 3.9 1.1 - - - -
213A ALA* 4.0 5.8 - - + -
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Residues in contact with GLU 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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42A ARG* 2.9 20.5 + - - -
88A ARG* 2.9 33.8 + - + +
89A ILE* 1.3 77.7 - - - +
91A ALA* 1.3 63.8 + - - +
154A LEU* 4.1 16.3 - - - +
155A GLY* 4.8 4.5 - - - +
212A ARG* 2.6 64.7 + - + +
214A THR* 2.7 27.5 + - - -
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Residues in contact with ALA 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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44A TRP* 5.2 3.4 - - + -
89A ILE* 3.7 1.4 - - - +
90A GLU* 1.3 81.0 - - - +
92A VAL* 1.3 70.3 + - - +
98A MET* 3.5 3.1 - - - +
154A LEU* 4.7 6.5 - - - -
210A GLY 3.8 10.5 - - - +
211A GLY* 3.3 2.3 - - - -
212A ARG* 2.9 52.9 + - + +
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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