Contacts of the helix formed by residues 2463 - 2472 (chain D) in PDB entry 6X34
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 PRO2463 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2459D ARG 3.8 3.6 - - - +
2460D SER* 4.3 10.1 - - - +
2461D LEU 3.3 11.4 - - - +
2462D VAL* 1.3 93.0 - - + +
2464D LEU* 1.3 65.8 + - - +
2465D ASP* 3.1 12.6 + - + +
2466D ASP* 3.4 18.0 + - + +
2467D LEU* 3.6 8.0 + - - +
2506D PHE* 5.2 0.3 - - - -
2511D TYR* 3.8 14.1 - - - +
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Residues in contact with LEU2464 (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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2463D PRO* 1.3 72.2 - - - +
2465D ASP* 1.3 59.6 + - - +
2466D ASP 3.4 0.2 - - - -
2467D LEU* 3.3 13.7 + - + +
2468D VAL* 2.9 33.1 + - + +
2507D LEU* 4.6 16.4 - - + -
2511D TYR* 3.6 54.6 + - + -
2519D LEU* 5.4 13.9 - - + -
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Residues in contact with ASP2465 (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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2378D LEU* 4.9 3.6 - - - +
2463D PRO* 3.1 10.1 - - + +
2464D LEU* 1.3 78.0 - - - +
2466D ASP* 1.3 59.1 + - - +
2468D VAL* 3.1 11.9 - - - +
2469D GLY* 2.9 26.5 + - - -
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Residues in contact with ASP2466 (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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2377D LEU* 3.7 28.8 - - + +
2378D LEU* 4.8 10.9 - - + +
2462D VAL* 3.6 26.7 - - + -
2463D PRO* 3.4 11.0 + - + +
2464D LEU 3.4 0.2 - - - -
2465D ASP* 1.3 78.4 - - - +
2467D LEU* 1.3 58.1 + - - +
2469D GLY* 3.8 1.2 - - - +
2470D ILE* 2.9 31.4 + - - +
2503D MET* 6.0 0.7 - - - -
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Residues in contact with LEU2467 (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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2462D VAL* 4.9 1.5 - - - +
2463D PRO 3.6 6.4 + - - +
2464D LEU* 3.3 19.2 + - + +
2465D ASP 3.2 0.6 - - - -
2466D ASP* 1.3 79.0 - - - +
2468D VAL* 1.3 56.8 + - - +
2470D ILE* 3.3 5.5 + - - +
2471D ILE* 2.9 34.9 + - + +
2503D MET* 5.2 9.8 - - + +
2506D PHE* 4.8 21.3 - - + -
2507D LEU* 4.4 21.8 - - + -
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Residues in contact with VAL2468 (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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2464D LEU 2.9 17.5 + - - +
2465D ASP* 3.1 22.2 - - - +
2467D LEU* 1.3 76.8 - - - +
2469D GLY* 1.3 57.0 + - - +
2471D ILE* 3.4 9.4 + - + +
2472D SER* 2.9 30.9 + - - -
2507D LEU* 5.5 3.3 - - + +
2519D LEU* 6.0 7.4 - - + -
2522D VAL* 3.7 29.8 - - + -
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Residues in contact with GLY2469 (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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2378D LEU* 3.5 30.9 - - - +
2465D ASP 2.9 13.6 + - - -
2466D ASP 3.8 0.4 - - - -
2468D VAL* 1.3 79.4 - - - +
2470D ILE* 1.3 59.8 + - - +
2472D SER* 3.4 12.9 + - - -
2473D LEU* 3.4 21.0 + - - +
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Residues in contact with ILE2470 (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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2377D LEU* 6.0 3.4 - - + -
2378D LEU* 3.8 4.8 - - + +
2381D ILE* 5.7 4.5 - - + -
2466D ASP 2.9 17.4 + - - +
2467D LEU 3.8 2.9 - - - +
2469D GLY* 1.3 73.7 - - - +
2471D ILE* 1.3 65.2 + - - +
2473D LEU* 3.4 33.1 + - + +
2495D PHE* 5.9 1.6 - - - -
2500D LYS* 4.6 5.4 - - - +
2503D MET* 3.8 37.3 - - + +
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Residues in contact with ILE2471 (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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2467D LEU* 2.9 22.5 + - + +
2468D VAL* 3.7 10.5 - - + +
2469D GLY 3.3 0.2 - - - -
2470D ILE* 1.3 77.1 - - - +
2472D SER* 1.3 56.5 + - - +
2473D LEU 3.1 5.1 + - - -
2500D LYS* 3.3 33.6 + - + +
2503D MET* 3.8 20.4 - - + -
2504D VAL* 3.7 31.9 - - + +
2507D LEU* 4.9 13.9 - - + -
2522D VAL 5.8 0.2 - - - +
2523D LEU* 6.2 1.1 - - - -
2526D GLY* 4.0 29.7 - - - +
2527D PHE* 4.4 18.6 - - + -
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Residues in contact with SER2472 (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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2468D VAL* 2.9 20.2 + - - -
2469D GLY* 3.8 9.2 - - - -
2470D ILE 3.3 0.4 - - - -
2471D ILE* 1.3 75.7 - - - +
2473D LEU* 1.3 63.9 + - - +
2474D PRO* 3.6 4.3 - - - +
2526D GLY* 5.0 11.4 - - - -
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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