Contacts of the helix formed by residues 115 - 123 (chain D) in PDB entry 2V5Q
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 THR 115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D HIS* 3.8 2.2 - - - -
106D VAL 4.3 1.3 - - - -
107D ASN* 3.6 22.8 + - - +
108D ALA 3.1 2.5 - - - -
109D PHE* 3.6 30.1 - - + -
114D SER* 1.3 75.8 - - - +
116D PRO* 1.3 75.5 - - - +
117D LEU* 3.5 11.6 + - - +
118D HIS* 2.9 42.5 + - + +
119D LEU* 3.3 11.4 + - - +
138D ASP 4.9 2.8 + - - -
141D ALA* 3.8 16.2 - - + -
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Residues in contact with PRO 116 (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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82D THR* 4.7 0.9 - - - +
84D LEU* 3.7 35.0 - - + +
85D HIS* 3.5 26.4 - - + +
88D ALA* 3.6 22.9 - - + +
105D ASP 4.8 1.3 - - - +
106D VAL 3.4 18.6 - - - +
108D ALA* 3.3 15.7 - - + +
115D THR* 1.3 82.4 - - - +
117D LEU* 1.3 55.7 + - - +
119D LEU* 3.4 3.2 + - + +
120D ALA* 2.9 29.8 + - - +
132D LEU* 3.7 9.0 - - + -
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Residues in contact with LEU 117 (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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126C LEU* 3.4 35.4 - - + -
106D VAL 5.1 1.0 + - - +
115D THR* 3.2 11.9 + - - +
116D PRO* 1.3 76.1 - - - +
118D HIS* 1.3 65.2 + - + +
120D ALA* 4.0 1.9 - - - +
121D ALA* 2.9 23.6 + - - +
129D VAL* 3.7 44.3 - - + +
132D LEU* 3.4 16.7 - - + +
133D LEU* 3.9 18.8 - - + -
137D ALA* 4.3 15.0 - - + -
138D ASP 4.8 2.9 - - - +
139D VAL* 4.2 21.3 - - + +
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Residues in contact with HIS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LEU* 3.4 28.4 - - + +
113D GLY 4.1 4.9 + - - -
114D SER* 3.6 22.2 - - - +
115D THR* 2.9 49.5 + - + +
117D LEU* 1.3 77.2 - - + +
119D LEU* 1.3 58.4 + - + +
121D ALA* 3.2 5.4 + - - +
122D ASP* 2.9 39.3 + - - +
138D ASP 5.3 0.4 + - - -
139D VAL 3.9 14.1 + - - -
141D ALA* 4.3 13.8 + - - +
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Residues in contact with LEU 119 (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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135A ARG* 4.1 13.7 - - - +
316A ILE* 5.1 12.1 - - + -
81D PHE* 3.7 11.4 - - + -
85D HIS* 3.4 30.1 - - + +
89D MET* 3.5 39.3 - - + -
110D ASP* 3.9 1.8 - - - +
114D SER* 3.6 24.0 - - - +
115D THR 3.3 10.7 + - - +
116D PRO* 3.7 6.5 - - + +
117D LEU 3.3 0.4 - - - -
118D HIS* 1.3 77.9 - - + +
120D ALA* 1.3 60.7 + - - +
122D ASP* 3.5 12.4 + - + +
123D GLU* 3.2 28.8 + - - +
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Residues in contact with ALA 120 (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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88D ALA 3.5 25.3 + - - +
89D MET* 4.7 0.9 - - - +
116D PRO 2.9 18.1 + - - +
117D LEU* 4.0 4.5 - - - +
119D LEU* 1.3 75.0 - - - +
121D ALA* 1.3 64.3 + - - +
123D GLU* 3.2 2.2 + - - +
124D GLY 3.1 3.6 + - - -
125D HIS* 2.9 38.0 + - + +
128D ILE* 3.8 21.8 - - + -
129D VAL* 4.1 6.1 - - + -
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Residues in contact with ALA 121 (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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121C ALA* 4.0 31.8 - - + +
122C ASP* 5.1 1.6 - - - -
124C GLY* 6.0 0.4 - - - -
126C LEU* 3.8 27.8 - - + -
129C VAL* 6.0 0.2 - - + -
117D LEU 2.9 19.1 + - - +
118D HIS* 3.5 4.7 - - - +
120D ALA* 1.3 76.0 - - - +
122D ASP* 1.3 64.7 + - - +
124D GLY* 3.1 13.7 + - - -
125D HIS 5.0 0.7 - - - +
126D LEU* 5.0 0.9 - - - -
129D VAL* 3.7 16.5 - - + +
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Residues in contact with ASP 122 (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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313A ARG* 3.8 31.6 + - - +
316A ILE* 5.7 3.6 - - + +
121C ALA 4.7 7.1 - - - +
122C ASP* 5.3 8.9 - - - +
124C GLY* 5.4 5.7 - - - -
114D SER* 5.8 0.2 + - - -
118D HIS* 2.9 24.5 + - - +
119D LEU* 3.7 14.8 - - - +
120D ALA 3.2 0.2 - - - -
121D ALA* 1.3 77.7 - - - +
123D GLU* 1.3 60.7 + - - +
124D GLY 3.3 1.0 + - - -
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Residues in contact with GLU 123 (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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313A ARG* 2.7 44.5 + - - +
315A PRO* 3.2 14.7 - - - +
316A ILE* 3.1 26.9 + - + +
317A THR* 4.7 2.4 - - + +
89D MET* 3.4 33.7 - - + +
119D LEU 3.2 14.8 + - - +
120D ALA 3.2 2.4 + - - +
121D ALA 3.2 0.6 - - - -
122D ASP* 1.3 77.0 - - - +
124D GLY* 1.3 61.2 + - - +
125D HIS* 3.3 21.5 + - + +
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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