Contacts of the helix formed by residues 2580 - 2593 (chain H) 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 VAL2580 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2520H LEU* 5.1 11.7 - - + -
2570H PHE* 4.4 23.0 - - + -
2579H MET* 1.3 73.5 - - - +
2581H ASP* 1.3 64.4 + - - +
2583H MET* 3.4 11.7 + - - +
2584H LEU* 3.4 23.8 - - + +
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Residues in contact with ASP2581 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2579H MET* 3.3 1.5 - - - +
2580H VAL* 1.3 79.5 - - - +
2582H SER* 1.3 60.4 + - - +
2584H LEU* 3.3 19.0 + - - +
2585H HIS* 3.9 5.0 + - - +
2623H LEU* 3.8 42.1 - - + +
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Residues in contact with SER2582 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2579H MET* 3.5 22.6 + - - +
2580H VAL 3.4 0.4 - - - -
2581H ASP* 1.3 76.3 - - - +
2583H MET* 1.3 63.6 + - - +
2584H LEU 3.2 0.2 - - - -
2585H HIS* 3.3 17.8 + - - +
2586H THR* 3.6 12.0 + - - +
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Residues in contact with MET2583 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2524H ASP* 6.0 6.3 - - + -
2579H MET 3.4 11.2 + - - +
2580H VAL* 3.7 12.8 - - - +
2581H ASP 3.2 1.2 - - - -
2582H SER* 1.3 77.7 - - - +
2584H LEU* 1.3 65.1 + - + +
2585H HIS 3.3 0.2 - - - -
2586H THR* 3.3 22.4 - - + +
2587H VAL* 3.7 9.7 + - - +
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Residues in contact with LEU2584 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2570H PHE* 5.0 15.5 - - + -
2580H VAL 3.4 17.3 - - - +
2581H ASP* 3.3 10.5 + - - +
2582H SER 3.2 0.8 - - - -
2583H MET* 1.3 81.2 - - + +
2585H HIS* 1.3 63.8 + - - +
2587H VAL* 3.7 10.7 + - + +
2588H TYR* 3.7 11.6 + - - +
2607H CYS* 6.5 0.4 - - - -
2608H LEU* 3.9 28.2 - - + +
2611H LEU* 4.6 25.8 - - + +
2615H ILE* 6.3 1.6 - - + -
2620H LEU* 6.2 4.0 - - + -
2623H LEU* 6.0 1.3 - - + -
2624H LEU* 5.3 15.3 - - + -
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Residues in contact with HIS2585 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2581H ASP 3.9 4.1 + - - +
2582H SER* 3.3 14.4 + - - +
2583H MET 3.3 1.0 - - - -
2584H LEU* 1.3 77.9 - - - +
2586H THR* 1.3 64.2 + - - +
2587H VAL 3.2 1.0 + - - -
2588H TYR* 3.3 8.8 + - - +
2589H ARG* 3.3 19.5 + - - +
2623H LEU* 6.3 1.1 - - + -
2627H LEU* 3.8 28.9 - - + -
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Residues in contact with THR2586 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2582H SER 3.6 7.5 + - - +
2583H MET* 3.3 26.0 - - + +
2585H HIS* 1.3 77.1 - - - +
2587H VAL* 1.3 64.6 + - + +
2589H ARG* 3.5 9.6 + - - +
2590H LEU* 3.4 32.4 + - - +
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Residues in contact with VAL2587 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2560H LEU* 6.0 4.3 - - + -
2583H MET 3.7 10.2 + - - +
2584H LEU* 3.9 7.2 - - + +
2585H HIS 3.2 0.4 - - - -
2586H THR* 1.3 82.4 - - - +
2588H TYR* 1.3 62.0 + - - +
2590H LEU* 3.5 8.1 + - - +
2591H SER* 3.4 14.4 + - - -
2604H ILE* 3.8 17.1 - - + +
2607H CYS* 5.3 10.1 - - + -
2608H LEU* 3.8 26.2 - - + +
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Residues in contact with TYR2588 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2584H LEU 3.7 8.7 + - - +
2585H HIS* 3.3 9.7 + - - +
2587H VAL* 1.3 76.7 - - - +
2589H ARG* 1.3 67.1 + - - +
2591H SER* 3.2 11.2 + - - -
2592H ARG* 3.1 34.6 + - + +
2608H LEU* 4.4 20.8 - - + +
2628H VAL* 3.5 36.3 - - + +
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Residues in contact with ARG2589 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2585H HIS 3.3 12.4 + - - +
2586H THR* 3.7 13.5 - - - +
2587H VAL 3.3 0.6 - - - -
2588H TYR* 1.3 81.8 - - - +
2590H LEU* 1.3 66.1 + - + +
2591H SER 3.5 0.2 + - - -
2592H ARG* 3.6 5.8 + - - +
2593H GLY* 3.5 15.4 + - - -
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Residues in contact with LEU2590 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2552H ASN* 5.1 12.7 + - - +
2555H LEU* 5.1 15.7 - - + -
2586H THR* 3.4 23.0 + - - +
2587H VAL* 4.0 9.0 - - - +
2588H TYR 3.3 0.4 - - - -
2589H ARG* 1.3 80.3 - - + +
2591H SER* 1.3 62.4 + - - +
2592H ARG 3.4 0.2 - - - -
2593H GLY* 3.6 13.3 + - - +
2596H LEU* 5.2 3.3 - - - +
2604H ILE* 4.1 23.2 - - + +
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Residues in contact with SER2591 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2587H VAL 3.4 6.6 + - - -
2588H TYR* 3.2 18.7 + - - -
2590H LEU* 1.3 77.7 - - - +
2592H ARG* 1.3 63.9 + - - +
2593H GLY 3.4 7.8 + - - +
2601H ARG* 6.0 0.4 - - - +
2604H ILE* 3.7 27.8 - - - +
2605H GLU* 5.6 2.9 - - - -
2608H LEU* 5.2 5.6 - - - -
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Residues in contact with ARG2592 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2588H TYR* 3.1 32.7 + - + +
2589H ARG* 4.0 7.2 - - - +
2590H LEU 3.4 0.2 - - - -
2591H SER* 1.3 75.3 - - - +
2593H GLY* 1.3 63.8 + - - +
2594H ARG* 3.6 2.4 + - - +
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Residues in contact with GLY2593 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2589H ARG 3.5 10.4 + - - -
2590H LEU* 3.6 10.6 + - - +
2591H SER 3.2 9.9 - - - +
2592H ARG* 1.3 81.0 - - - +
2594H ARG* 1.3 62.2 + - - -
2595H SER* 3.4 7.6 + - - -
2596H LEU* 4.6 8.1 - - - +
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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