Contacts of the helix formed by residues 86 - 99 (chain A) in PDB entry 1V2E
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 GLY 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A THR* 2.7 34.3 + - - -
85A SER* 1.3 72.4 - - - +
87A ALA* 1.3 62.2 + - - -
88A THR 2.9 6.8 + - - -
89A GLU 3.2 9.2 + - - -
90A ALA 3.3 0.3 + - - -
230A ARG* 3.4 12.9 + - - -
231A VAL 4.0 0.4 - - - -
232A GLY* 3.3 14.0 - - - +
510A PLP 3.6 15.5 - - - -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 4.6 0.2 - - - -
86A GLY* 1.3 73.9 - - - -
88A THR* 1.3 54.6 + - - +
90A ALA* 3.1 9.5 + - - +
91A LEU* 3.0 34.7 + - - +
193A VAL* 3.5 27.4 - - + -
217A VAL* 3.7 12.8 - - + -
218A GLY 3.8 7.9 - - - +
219A SER* 3.9 0.4 - - - -
232A GLY* 4.0 3.0 - - - -
510A PLP 2.9 34.0 + - + +
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLY 2.9 0.2 - - - -
87A ALA* 1.3 78.3 - - - +
89A GLU* 1.3 57.8 + - - +
91A LEU* 3.5 7.5 + - - +
92A TYR* 3.2 24.1 + - - +
112A PHE* 5.7 0.3 - - - -
114A VAL* 4.8 18.3 - - + +
118A ASP* 4.3 1.0 - - - +
230A ARG* 3.5 12.7 + - - -
510A PLP 2.8 32.5 + - - -
520A KMT 5.0 4.3 - - - +
249B GLN 3.8 6.7 - - - +
250B TRP* 3.6 13.0 - - - +
251B THR 3.3 15.0 - - - +
252B SER 4.3 0.2 - - - -
253B PHE* 3.6 25.8 - - + +
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Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 3.2 7.0 - - - +
85A SER* 2.7 38.2 + - - +
86A GLY 3.2 4.6 + - - +
88A THR* 1.3 75.3 - - - +
90A ALA* 1.3 64.5 + - - +
92A TYR* 3.9 2.5 - - + -
93A VAL* 3.1 28.8 + - + +
248A ARG* 2.6 31.1 + - - +
251A THR* 3.0 23.4 + - + +
252A SER* 2.4 29.5 + - - -
89B GLU* 5.5 0.3 - - - +
251B THR* 2.9 21.0 + - - +
252B SER* 4.4 2.3 - - - -
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 3.6 24.7 + - - +
86A GLY 3.3 4.7 + - - +
87A ALA* 3.1 15.4 + - - +
89A GLU* 1.3 78.8 - - - +
91A LEU* 1.3 57.2 - - - +
93A VAL* 3.9 0.9 - - - +
94A LEU* 2.9 37.7 + - - +
217A VAL* 4.0 15.7 - - + -
233A TRP 4.5 2.0 - - - +
234A ILE* 3.9 20.9 - - + -
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA 3.0 19.1 + - - +
88A THR* 3.9 4.7 - - - +
90A ALA* 1.3 76.2 - - - +
92A TYR* 1.3 63.8 + - - +
94A LEU* 3.6 3.2 - - + +
95A LEU* 3.2 31.3 + - + +
112A PHE* 4.7 4.5 - - + -
114A VAL* 4.7 9.0 - - + -
115A TYR* 3.7 26.5 - - + -
118A ASP* 3.5 8.4 - - - +
157A LEU* 5.1 3.4 - - + -
189A ILE* 4.1 25.6 - - + -
191A ASP* 3.1 30.1 - - + +
217A VAL* 4.2 17.3 - - + -
510A PLP 4.1 13.0 - - + -
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Residues in contact with TYR 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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88A THR 3.2 9.8 + - - +
89A GLU* 4.2 2.7 - - + +
90A ALA 3.4 0.2 - - - -
91A LEU* 1.3 78.0 - - - +
93A VAL* 1.3 70.7 + - + +
95A LEU* 3.5 2.1 + - - +
96A GLN* 3.0 52.1 + - + +
118A ASP* 2.9 32.3 + - + +
121A LEU* 4.0 29.7 - - + +
251A THR* 3.9 16.8 - - + -
92B TYR* 2.2 42.8 + + - -
96B GLN* 4.0 8.7 + - - +
250B TRP 3.4 24.5 - - - +
251B THR* 4.1 17.9 - - + +
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 6.0 0.7 - - + -
89A GLU* 3.1 23.6 + - + +
90A ALA* 4.2 2.9 - - - +
92A TYR* 1.3 87.0 - - + +
94A LEU* 1.3 66.3 + - - +
96A GLN* 3.6 7.9 - - - +
97A SER* 3.1 18.9 + - - -
234A ILE* 5.3 4.3 - - + -
244A LEU* 4.2 16.3 - - + +
247A MET* 3.3 29.8 - - + -
248A ARG* 3.8 27.4 - - + +
251A THR* 4.0 12.1 - - + -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ALA 2.9 13.9 + - - +
91A LEU* 3.6 7.6 - - - +
92A TYR 3.1 0.2 - - - -
93A VAL* 1.3 73.7 - - - +
95A LEU* 1.3 57.7 + - - +
96A GLN 3.0 0.9 - - - -
97A SER* 2.6 28.4 + - - -
98A LEU* 3.1 18.4 + - + +
189A ILE* 3.6 43.5 - - + -
215A PHE* 4.1 16.6 - - + -
217A VAL* 3.8 22.7 - - + -
234A ILE* 3.5 36.6 - - + -
244A LEU* 3.8 20.4 - - + -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.2 13.9 + - + +
92A TYR 4.0 2.7 - - - +
94A LEU* 1.3 78.4 - - - +
96A GLN* 1.3 62.8 + - - +
98A LEU* 3.1 3.3 + - + +
99A VAL* 3.1 51.4 + - + +
105A VAL* 4.1 24.0 - - + -
115A TYR* 3.9 8.1 - - + +
118A ASP* 3.3 39.5 - - + +
119A ALA* 3.7 16.6 - - + +
122A ALA* 4.0 1.5 - - + +
155A ALA* 6.1 0.4 - - + -
157A LEU* 4.4 21.5 - - + -
189A ILE* 4.3 14.5 - - + +
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Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR* 3.0 37.7 + - + +
93A VAL* 3.6 11.2 - - - +
94A LEU 3.0 0.6 - - - -
95A LEU* 1.3 78.0 - - - +
97A SER* 1.3 57.7 + - - +
98A LEU 3.7 0.2 + - - -
99A VAL 3.9 0.5 - - - +
118A ASP 5.2 0.9 - - - +
121A LEU 3.6 21.0 + - - +
122A ALA* 4.1 10.7 - - - +
247A MET* 3.2 24.6 - - + +
4B HIS* 4.3 2.6 - - - +
6B ARG* 3.2 48.5 + - - +
92B TYR* 3.2 23.6 + - - -
96B GLN* 4.2 9.9 - - - +
121B LEU* 4.5 10.3 + - - +
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Residues in contact with SER 97 (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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93A VAL 3.1 8.9 + - - -
94A LEU 2.6 14.7 + - - -
96A GLN* 1.3 71.7 - - - +
98A LEU* 1.3 67.9 + - - +
243A ARG 5.5 0.2 - - - -
244A LEU* 3.5 21.2 - - - +
247A MET* 3.1 31.9 - - - +
3B LEU* 3.6 7.7 - - - +
4B HIS* 2.9 23.6 + - - -
7B THR* 3.8 17.3 - - - +
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Residues in contact with LEU 98 (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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94A LEU* 3.6 15.5 - - + +
95A LEU* 3.1 5.3 + - - +
97A SER* 1.3 93.4 - - - +
99A VAL* 1.3 70.5 + - + +
103A ASP* 4.6 1.2 - - - +
154A ARG* 3.9 18.2 - - - +
155A ALA* 4.9 4.0 - - + -
187A PHE* 3.8 42.1 - - + -
189A ILE* 3.9 31.4 - - + -
215A PHE* 4.1 17.5 - - + -
244A LEU* 5.8 1.3 - - + -
2B ARG* 5.4 2.1 + - - +
3B LEU* 3.2 26.0 - - + -
4B HIS* 4.2 9.2 + - - +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.1 31.8 + - + +
98A LEU* 1.3 85.3 - - + +
100A GLY* 1.3 52.7 + - - +
103A ASP* 3.8 7.4 - - + -
104A GLU 4.3 7.2 - - - +
105A VAL* 3.4 22.9 - - + -
119A ALA 5.0 0.4 - - - +
122A ALA* 3.8 12.1 - - + -
124A ALA* 3.4 22.7 - - + -
154A ARG* 4.3 9.6 - - + -
155A ALA* 4.4 11.4 - - + -
4B HIS* 2.9 10.4 - - - +
6B ARG* 2.4 31.5 + - - -
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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