Contacts of the helix formed by residues 10 - 17 (chain B) in PDB entry 1XV2
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 10 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 3.0 18.7 - - + +
164A PHE* 3.8 24.5 - - + -
9B GLY* 1.3 79.5 - - - +
11B LEU* 1.3 62.5 + - - +
13B THR* 2.9 29.9 + - - +
14B LEU* 3.2 19.6 + - - +
72B PRO 5.2 0.4 + - - +
73B TYR* 3.5 10.5 - - - +
167B VAL* 3.5 14.6 - - + +
207B GLN* 3.6 22.7 - - - +
209B PHE* 4.8 5.8 - - + -
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 1.3 72.5 - - - +
12B GLY* 1.3 61.1 + - - +
14B LEU* 3.0 18.7 + - + +
15B MSE 2.8 48.6 + - + +
73B TYR* 3.4 31.7 - - + +
136B LEU* 5.5 0.7 - - + -
166B GLY 3.8 6.3 - - - +
167B VAL 3.3 6.2 + - - +
168B GLY 4.0 5.2 - - - +
169B SER* 3.6 38.1 - - - +
173B HIS* 5.2 4.9 - - + +
230B ILE* 4.1 20.9 - - + -
234B GLU 4.4 15.9 - - - +
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Residues in contact with GLY 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 4.0 11.9 - - - -
10B THR* 3.4 0.6 + - - -
11B LEU* 1.3 73.9 - - - +
13B THR* 1.3 59.8 + - - +
15B MSE 3.3 4.8 + - - +
16B ALA* 3.1 17.7 + - - +
166B GLY* 2.7 25.5 + - - -
223B TYR* 3.6 16.0 - - - -
226B VAL* 4.0 19.2 - - - +
230B ILE* 5.0 0.9 - - - -
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Residues in contact with THR 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 3.9 1.0 - - - +
9B GLY* 6.4 0.2 - - - -
10B THR* 2.9 28.2 + - - +
11B LEU 3.2 0.6 - - - -
12B GLY* 1.3 73.8 - - - +
14B LEU* 1.3 65.8 + - - +
16B ALA* 3.2 16.1 + - - +
17B GLY 3.5 4.3 + - - -
18B LEU* 3.5 40.3 + - + +
216B PHE* 4.1 18.3 - - + -
221B ILE* 4.1 4.6 - - + +
223B TYR* 3.0 26.3 + - - -
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR 3.2 14.4 + - - +
11B LEU* 3.0 16.4 + - + +
13B THR* 1.3 76.1 - - - +
15B MSE 1.3 64.1 + - - +
17B GLY* 3.0 11.4 + - - -
18B LEU 3.8 8.1 - - - +
19B LEU* 3.4 35.9 - - + +
38B THR* 4.4 13.0 - - + -
42B SER* 4.7 2.2 - - - +
72B PRO* 3.5 34.5 - - + +
73B TYR* 4.0 28.3 - - + -
136B LEU* 3.7 26.2 - - + +
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Residues in contact with MSE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 2.8 29.6 + - + +
12B GLY 3.5 8.3 - - - +
14B LEU* 1.3 78.6 - - - +
16B ALA* 1.3 60.8 + - - +
17B GLY 3.1 1.6 + - - -
135B ARG* 3.0 17.7 - - - -
136B LEU* 3.2 39.0 + - - -
137B ILE* 4.7 7.1 + - + +
226B VAL* 3.8 12.6 - - + -
229B GLU* 3.0 55.3 - - + +
230B ILE* 3.4 26.2 - - + +
233B ALA* 3.9 14.1 - - + -
234B GLU 5.2 5.2 - - - +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY 3.1 11.9 + - - +
13B THR 3.4 8.5 - - - +
14B LEU 3.2 0.4 - - - -
15B MSE 1.3 75.7 - - - +
17B GLY* 1.3 56.4 + - - +
18B LEU* 3.8 5.6 - - + +
134B THR 4.7 0.2 - - - -
135B ARG* 2.9 35.8 + - - +
221B ILE* 3.3 34.8 - - + -
222B ASP 3.6 14.4 - - - +
223B TYR* 4.6 0.7 - - + -
226B VAL* 5.3 0.6 - - - +
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU 3.0 11.7 + - - -
15B MSE 3.0 1.2 - - - -
16B ALA* 1.3 80.3 - - - +
18B LEU* 1.3 56.2 + - - +
19B LEU* 2.7 27.7 + - - +
133B TYR* 3.2 16.6 - - - +
134B THR* 3.4 23.8 - - - -
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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