Contacts of the helix formed by residues 95 - 103 (chain A) in PDB entry 1V9P
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A TYR* 3.2 24.9 - - + +
92A GLU* 3.1 20.6 - - - +
93A GLU 2.9 3.2 + - - -
94A VAL* 1.3 76.3 - - - +
96A ALA* 1.3 59.8 + - - +
97A PHE 3.0 0.4 - - - -
98A GLU* 3.0 4.4 + - + +
99A GLU* 2.6 64.3 + - - +
109A ARG* 3.0 33.9 - - - +
264A ALA* 3.9 9.6 - - + -
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Residues in contact with ALA 96 (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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92A GLU 2.7 17.0 + - - +
93A GLU* 4.2 9.0 - - + -
95A LEU* 1.3 78.5 - - - +
97A PHE* 1.3 50.6 + - - +
99A GLU* 2.9 14.2 + - - +
100A ARG* 2.6 36.3 + - - +
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Residues in contact with PHE 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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94A VAL* 3.4 27.5 - - + +
95A LEU 3.0 0.2 - - - -
96A ALA* 1.3 78.8 - - - +
98A GLU* 1.3 61.1 + - + +
100A ARG* 2.9 52.5 + - - +
101A LEU* 3.2 26.2 + - + +
113A TYR* 4.3 14.6 - + - -
290A VAL* 4.6 11.9 - - + -
309A ARG 3.0 29.4 - - - -
310A PHE 3.9 2.9 - - - -
311A ALA 3.5 32.5 - - - -
312A LEU* 3.4 28.7 - - + -
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Residues in contact with GLU 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 VAL 3.8 9.1 + - - +
95A LEU 3.0 8.6 + - - +
97A PHE* 1.3 80.3 - - + +
99A GLU* 1.3 61.1 + - - +
101A LEU* 3.2 8.4 + - - +
102A GLU* 3.2 19.1 + - - +
109A ARG* 2.3 51.2 - - + +
111A PHE* 2.8 25.5 + - + +
113A TYR* 3.0 25.0 + - + +
263A GLY* 3.0 8.4 - - - -
264A ALA* 2.6 32.1 + - + +
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Residues in contact with GLU 99 (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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95A LEU* 2.6 40.4 + - - +
96A ALA* 3.0 17.5 - - - +
98A GLU* 1.3 72.2 - - - +
100A ARG* 1.3 54.9 + - - +
102A GLU* 2.6 58.2 + - + +
103A ARG* 3.7 6.7 + - - -
109A ARG* 3.4 20.3 + - - +
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Residues in contact with ARG 100 (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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86A ASP* 4.9 15.8 + - - +
96A ALA 2.6 16.4 + - - +
97A PHE* 3.1 33.6 - - - +
99A GLU* 1.3 71.2 - - - +
101A LEU* 1.3 58.6 + - - +
103A ARG* 2.8 33.4 + - + +
301A LEU* 5.9 1.2 - - - +
304A THR* 5.1 5.7 - - - +
308A PRO 4.2 4.4 + - - -
309A ARG* 3.6 51.9 + - - +
312A LEU* 5.6 2.2 - - - +
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Residues in contact with LEU 101 (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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97A PHE* 3.6 21.1 - - + +
98A GLU* 3.3 7.6 - - - +
99A GLU 3.0 0.8 - - - -
100A ARG* 1.3 78.1 - - - +
102A GLU* 1.3 66.4 + - - +
103A ARG 3.0 11.8 + - - +
104A ALA* 4.0 6.9 - - - +
105A LEU 4.4 1.4 + - - -
111A PHE* 4.5 17.6 - - + -
113A TYR* 3.3 32.1 - - + +
292A LEU* 3.7 23.1 - - + -
301A LEU* 3.5 36.6 - - + +
309A ARG 3.5 22.2 - - - +
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Residues in contact with GLU 102 (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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98A GLU 3.2 13.6 + - - +
99A GLU* 2.6 54.7 + - + +
101A LEU* 1.3 72.2 - - - +
103A ARG* 1.3 51.4 + - - +
104A ALA 2.5 18.5 + - - -
105A LEU* 3.0 32.9 + - + +
108A LYS 3.1 24.4 - - - +
109A ARG* 3.2 27.6 - - + +
111A PHE* 4.7 3.8 - - + -
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Residues in contact with ARG 103 (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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99A GLU 3.9 9.4 - - - -
100A ARG* 2.8 28.2 - - + +
101A LEU 3.0 3.2 - - - +
102A GLU* 1.3 75.0 - - - +
104A ALA* 1.3 67.2 + - - +
301A LEU* 6.2 0.5 - - - +
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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