Contacts of the helix formed by residues 14 - 23 (chain D) in PDB entry 2V1T
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 ARG 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D GLY 3.0 2.3 + - - -
13D PRO* 1.3 78.4 - - + +
15D LEU* 1.3 58.8 + - - +
16D SER* 3.0 10.5 - - - +
17D ARG* 3.1 54.0 + - + +
18D LEU* 4.1 0.9 + - - +
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Residues in contact with LEU 15 (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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78B GLU* 3.5 38.6 - - + +
113B THR* 5.0 18.4 - - + +
12D GLY 2.8 23.3 + - - +
14D ARG* 1.3 76.5 - - - +
16D SER* 1.3 61.4 + - - +
17D ARG 3.1 0.4 - - - -
18D LEU* 3.1 43.2 + - + +
19D LEU* 3.3 15.2 + - + +
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Residues in contact with SER 16 (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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71B LEU 5.1 0.4 - - - -
74B ILE* 3.7 29.8 - - - +
75B GLN* 4.3 21.1 + - - -
78B GLU* 4.9 2.2 - - - +
13D PRO 3.0 18.5 + - - -
14D ARG* 3.0 4.9 - - - -
15D LEU* 1.3 78.3 - - - +
17D ARG* 1.3 61.3 + - - +
19D LEU* 4.4 6.1 - - - -
20D SER* 2.8 32.6 + - - -
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Residues in contact with ARG 17 (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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14D ARG* 3.1 45.1 + - + +
16D SER* 1.3 81.3 + - - +
18D LEU* 1.3 61.6 + - - +
20D SER* 3.2 8.9 + - - +
21D ALA* 3.1 25.6 + - - +
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Residues in contact with LEU 18 (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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109B VAL* 3.8 23.1 - - + +
113B THR* 4.0 20.6 - - + -
14D ARG 4.1 0.8 + - - +
15D LEU* 3.1 33.7 + - + +
17D ARG* 1.3 79.5 - - - +
19D LEU* 1.3 62.0 + - + +
21D ALA* 3.4 10.1 + - + +
22D ALA* 3.3 17.3 + - - +
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Residues in contact with LEU 19 (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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70B PHE* 4.7 3.4 - - - -
74B ILE* 4.1 31.2 - - + +
78B GLU* 3.5 23.3 - - - +
93B LEU* 4.5 6.5 - - + -
106B LEU* 3.6 23.4 - - + +
109B VAL* 3.7 24.7 - - + -
110B LEU* 3.8 29.6 - - + -
113B THR* 4.6 5.6 - - - +
15D LEU* 3.3 13.7 + - + +
16D SER* 3.3 9.9 + - - +
18D LEU* 1.3 79.6 - - + +
20D SER* 1.3 61.1 + - - +
22D ALA* 3.2 20.6 + - - +
23D GLY 4.0 1.9 + - - +
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Residues in contact with SER 20 (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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55A PRO* 5.5 3.8 - - - +
70B PHE* 4.2 13.4 - - - -
71B LEU* 4.0 27.7 - - - +
74B ILE* 4.0 3.5 - - - +
16D SER 2.8 21.9 + - - -
17D ARG* 3.2 12.0 + - - -
19D LEU* 1.3 72.9 - - - +
21D ALA* 1.3 62.5 + - - +
23D GLY* 3.1 16.0 + - - +
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Residues in contact with ALA 21 (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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105B GLN* 5.0 1.0 - - - +
17D ARG 3.1 19.1 + - - +
18D LEU* 3.5 11.2 - - + +
19D LEU 3.3 0.2 - - - -
20D SER* 1.3 74.1 + - - +
22D ALA* 1.3 64.1 + - - +
23D GLY* 3.0 3.9 + - - -
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Residues in contact with ALA 22 (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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54A GLY 5.6 1.2 + - - -
105B GLN* 3.1 37.8 - - + +
106B LEU* 3.6 32.1 - - + +
109B VAL* 4.3 10.8 - - + -
18D LEU 3.3 8.0 + - - +
19D LEU 3.2 14.7 + - - +
21D ALA* 1.3 77.4 - - - +
23D GLY* 1.3 62.8 + - - +
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Residues in contact with GLY 23 (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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54A GLY* 3.2 19.5 - - - -
55A PRO* 4.7 3.8 - - - -
56A LEU 5.1 0.4 - - - -
70B PHE* 5.5 3.0 - - - -
100B CYS* 3.7 4.0 - - - -
102B GLN 4.2 4.1 - - - +
105B GLN* 5.3 0.3 - - - +
106B LEU* 4.4 8.0 + - - +
19D LEU 4.0 2.1 + - - +
20D SER* 3.1 14.8 + - - -
21D ALA 3.0 5.1 - - - -
22D ALA* 1.3 87.3 - - - +
24D CY3 1.3 65.2 + - - -
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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