Contacts of the helix formed by residues 2453 - 2464 (chain B) 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 GLY2453 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2450B GLU 4.9 1.5 + - - -
2451B GLY 3.5 6.5 + - - -
2452B LEU* 1.3 75.7 - - - +
2454B GLU* 1.3 67.2 + - - -
2455B LYS* 3.1 5.8 - - - -
2456B LEU* 2.8 20.6 + - - +
2457B ILE* 2.9 13.9 + - - +
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Residues in contact with GLU2454 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2435B PHE* 3.5 31.5 - - + -
2439B ARG* 4.1 33.1 + - + -
2452B LEU 4.0 0.6 + - - -
2453B GLY* 1.3 70.6 - - - -
2455B LYS* 1.3 61.4 + - + +
2457B ILE* 4.5 5.6 - - - +
2458B GLU* 3.0 39.6 + - - +
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Residues in contact with LYS2455 (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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2453B GLY* 3.1 2.4 - - - -
2454B GLU* 1.3 79.9 - - + +
2456B LEU* 1.3 61.4 + - - +
2458B GLU* 4.2 5.4 - - - +
2459B ARG* 3.2 22.7 + - - +
2485B ARG* 3.6 23.3 + - - +
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Residues in contact with LEU2456 (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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2451B GLY 3.7 11.7 - - - +
2452B LEU* 3.4 22.2 - - + -
2453B GLY* 2.8 13.8 + - - +
2455B LYS* 1.3 75.6 - - - +
2457B ILE* 1.3 53.5 + - - +
2459B ARG* 2.7 5.7 + - - +
2460B LEU* 2.6 55.5 + - + +
2481B LEU* 4.6 7.6 - - + -
2484B GLU* 3.8 28.3 - - + +
2485B ARG* 3.7 17.8 - - - +
2486B MET* 4.5 15.5 - - + -
2494B LEU* 3.5 20.4 - - + -
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Residues in contact with ILE2457 (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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2435B PHE* 4.3 14.1 - - + +
2438B ILE* 3.6 26.5 - - + -
2439B ARG* 3.5 38.1 - - + +
2442B ALA* 5.0 1.3 - - + -
2452B LEU* 3.4 37.2 - - + +
2453B GLY 2.9 15.7 + - - +
2454B GLU* 3.9 6.1 - - - +
2456B LEU* 1.3 74.2 - - - +
2458B GLU* 1.3 58.1 + - - +
2460B LEU* 2.6 33.5 + - + +
2461B LEU* 2.9 32.7 + - + +
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Residues in contact with GLU2458 (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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2435B PHE* 3.6 26.1 - - + -
2454B GLU* 3.0 19.4 + - - +
2455B LYS* 4.2 4.4 - - - +
2457B ILE* 1.3 80.2 - - - +
2459B ARG* 1.3 59.5 + - - +
2461B LEU* 3.9 12.4 + - - +
2462B GLU* 3.8 16.6 + - - +
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Residues in contact with ARG2459 (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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2455B LYS 3.2 14.2 + - - +
2456B LEU 2.7 14.3 + - - +
2457B ILE 2.7 3.6 + - - -
2458B GLU* 1.3 72.4 - - - +
2460B LEU* 1.3 63.1 + - - +
2461B LEU 3.2 1.6 - - - -
2462B GLU* 3.3 17.8 + - - +
2463B LYS* 3.1 34.2 + - + +
2484B GLU* 3.1 27.4 - - + +
2485B ARG* 4.1 9.4 - - - +
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Residues in contact with LEU2460 (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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2438B ILE* 6.2 0.2 - - + -
2452B LEU* 3.5 31.9 - - + -
2456B LEU* 2.6 34.3 + - + +
2457B ILE* 2.6 14.0 + - + +
2459B ARG* 1.3 72.1 - - - +
2461B LEU* 1.3 59.5 + - + +
2463B LYS 3.6 0.2 + - - -
2464B GLY 3.2 3.6 + - - -
2465B LEU* 2.9 62.8 + - + +
2466B VAL* 3.6 23.7 + - + -
2472B LEU* 4.8 5.6 - - + -
2475B LEU* 4.7 9.2 - - + -
2481B LEU* 4.2 19.1 - - + -
2484B GLU* 4.3 4.9 - - - +
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Residues in contact with LEU2461 (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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2434B ARG* 4.1 30.3 - - + -
2435B PHE* 4.7 12.1 - - + +
2438B ILE* 4.7 3.6 - - + -
2457B ILE* 2.9 52.3 + - + +
2458B GLU* 3.9 11.4 - - - +
2459B ARG 3.2 0.2 - - - -
2460B LEU* 1.3 78.6 - - + +
2462B GLU* 1.3 61.4 + - - +
2464B GLY* 3.2 13.3 + - - -
2466B VAL* 3.3 37.4 - - + +
2467B ARG* 4.3 2.9 - - - +
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Residues in contact with GLU2462 (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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2458B GLU 3.8 9.0 + - - +
2459B ARG* 3.3 22.2 + - - +
2461B LEU* 1.3 74.8 - - - +
2463B LYS* 1.3 62.7 + - + +
2464B GLY* 2.9 7.4 + - - -
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Residues in contact with LYS2463 (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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2459B ARG* 3.1 31.5 + - + +
2460B LEU 4.2 0.2 - - - +
2462B GLU* 1.3 76.2 - - - +
2464B GLY* 1.3 60.4 + - - +
2465B LEU* 3.8 28.4 - - + +
2480B LEU* 4.0 7.3 + - - +
2483B LEU* 3.9 29.7 + - - +
2484B GLU* 3.0 33.9 + - + +
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Residues in contact with GLY2464 (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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2461B LEU 3.2 13.6 + - - -
2462B GLU 2.9 5.3 - - - -
2463B LYS* 1.3 82.3 - - - +
2465B LEU* 1.3 65.2 + - - +
2466B VAL 3.5 3.8 - - - -
2467B ARG* 6.4 0.7 - - - -
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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