Contacts of the helix formed by residues 2505 - 2514 (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 GLY2505 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2447B MET* 4.6 2.1 - - - +
2502B LYS 5.2 0.4 + - - -
2503B HIS 3.1 5.4 + - - -
2504B ARG* 1.3 82.4 - - - +
2506B LEU* 1.3 67.0 + - - -
2507B GLU* 3.1 10.8 - - - -
2508B ARG* 3.7 0.9 + - - +
2509B LEU* 3.0 23.6 + - - +
2580B SER* 5.0 14.1 - - - -
2582B GLU 3.8 8.3 - - - -
2584B LYS* 4.2 6.1 - - - -
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Residues in contact with LEU2506 (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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2505B GLY* 1.3 68.3 - - - -
2507B GLU* 1.3 65.0 + - - +
2509B LEU* 2.6 37.5 + - + +
2510B LEU* 2.7 39.0 + - + +
2527B ALA* 3.5 20.2 - - + +
2530B PHE* 5.9 0.4 - - + -
2531B GLY 3.1 36.1 - - - +
2532B THR* 3.6 8.3 - - - +
2533B MET* 4.4 12.3 - - + +
2536B LEU* 6.4 0.4 - - + -
2581B MET 3.0 24.9 - - - +
2582B GLU 3.0 7.3 + - - +
2583B SER* 3.4 15.5 - - - +
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Residues in contact with GLU2507 (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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2504B ARG 3.4 5.9 - - - +
2505B GLY* 3.1 4.4 - - - -
2506B LEU* 1.3 97.0 + - - +
2508B ARG* 1.3 90.6 + - + +
2510B LEU* 3.3 1.3 + - - -
2511B TYR* 3.2 16.1 + - - +
2523B ALA* 3.5 18.2 - - + +
2524B ARG* 4.3 26.9 - - + +
2527B ALA* 3.5 15.1 - - + +
2528B ARG* 5.6 5.6 - - - +
2583B SER* 3.7 4.0 - - - -
2584B LYS* 2.9 34.9 + - - +
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Residues in contact with ARG2508 (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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2444B ARG 3.9 2.6 + - - -
2445B LYS* 3.3 23.9 + - - +
2446B ALA 3.4 23.9 + - - +
2447B MET* 3.7 2.0 - - - +
2448B ASP* 3.6 20.4 + - - +
2504B ARG* 3.3 56.9 + - + +
2505B GLY 4.1 0.7 - - - +
2506B LEU 3.2 0.4 - - - -
2507B GLU* 1.3 99.5 + - + +
2509B LEU* 1.3 57.6 + - - +
2511B TYR* 3.5 6.5 + - - +
2512B ALA* 2.8 29.5 + - - +
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Residues in contact with LEU2509 (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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2441B TYR* 4.0 25.1 - - + +
2447B MET* 3.7 13.4 - - + -
2505B GLY 3.0 16.2 + - - +
2506B LEU* 2.6 27.7 + - + +
2508B ARG* 1.3 69.6 - - - +
2510B LEU* 1.3 67.2 + - + +
2512B ALA 2.9 9.7 + - - -
2513B LEU* 2.9 45.0 + - + +
2533B MET* 5.1 7.6 - - + -
2571B VAL* 5.7 0.2 - - + -
2574B LEU* 4.2 7.0 - - + -
2579B VAL* 4.5 5.2 - - + -
2580B SER 3.7 21.8 - - - +
2581B MET* 4.0 21.5 - - + -
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Residues in contact with LEU2510 (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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2506B LEU* 2.7 30.6 + - + +
2507B GLU 3.6 7.2 - - - +
2509B LEU* 1.3 73.9 - - + +
2511B TYR* 1.3 62.3 + - - +
2513B LEU* 3.5 12.3 + - + +
2514B GLY 3.7 6.6 + - - -
2515B LEU* 4.1 19.8 - - + +
2518B VAL* 4.0 14.8 - - + +
2523B ALA* 4.0 10.5 - - + +
2526B LEU* 3.6 15.5 - - + -
2527B ALA* 3.3 44.0 - - + +
2533B MET* 4.4 13.5 - - + -
2536B LEU* 3.8 27.1 - - + -
2567B PHE* 6.0 0.2 - - + -
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Residues in contact with TYR2511 (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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2440B HIS* 3.0 44.1 + + - -
2443B SER* 4.7 3.1 + - - -
2445B LYS* 3.7 42.4 - - + +
2446B ALA* 3.9 8.3 - - - -
2507B GLU 3.2 11.0 + - - +
2508B ARG* 3.8 7.6 - - - +
2509B LEU 3.1 0.4 - - - -
2510B LEU* 1.3 78.7 - - - +
2512B ALA* 1.3 63.2 + - - +
2513B LEU 3.2 1.2 + - - -
2514B GLY* 3.2 10.8 + - - -
2518B VAL* 3.9 18.2 - - - -
2519B GLY* 4.0 16.8 - - - -
2520B GLU* 4.3 24.8 + - + +
2523B ALA* 3.8 14.5 - - + +
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Residues in contact with ALA2512 (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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2437B ALA 4.7 2.6 - - - +
2440B HIS* 4.2 7.2 - - - +
2441B TYR* 3.6 32.0 + - + +
2446B ALA* 3.8 19.7 - - + -
2447B MET* 3.3 31.0 - - + -
2469B VAL* 5.5 0.7 - - - +
2508B ARG 2.8 20.7 + - - +
2509B LEU 2.9 5.1 + - - +
2511B TYR* 1.3 77.3 - - - +
2513B LEU* 1.3 60.6 + - - +
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Residues in contact with LEU2513 (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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2428B PRO* 6.4 0.4 - - + -
2440B HIS* 6.2 0.2 - - - -
2441B TYR* 4.6 3.8 - - + -
2469B VAL* 4.6 11.0 - - + -
2509B LEU* 2.9 51.4 + - + +
2510B LEU* 3.9 7.2 - - + +
2511B TYR 3.1 0.4 - - - -
2512B ALA* 1.3 80.3 - - - +
2514B GLY* 1.3 63.5 + - - +
2515B LEU* 4.1 14.9 - - + +
2533B MET* 5.4 4.3 - - + -
2567B PHE* 3.8 21.1 - - + -
2570B LEU* 3.5 32.5 - - + -
2571B VAL* 6.2 1.1 - - + -
2574B LEU* 4.0 10.8 - - + -
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Residues in contact with GLY2514 (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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2440B HIS* 5.1 11.2 - - - -
2510B LEU 3.7 2.0 + - - -
2511B TYR 3.2 13.9 + - - -
2512B ALA 3.4 0.4 - - - -
2513B LEU* 1.3 80.6 - - - +
2515B LEU* 1.3 68.0 + - - +
2516B PRO* 3.8 2.4 - - - +
2518B VAL* 4.6 5.2 - - - -
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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