Contacts of the helix formed by residues 677 - 685 (chain B) in PDB entry 6A5T
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 GLY 677 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA* 4.9 5.2 - - - -
27B GLU* 4.3 2.5 - - - -
655B ILE* 4.5 10.2 - - - +
675B VAL* 4.1 7.6 - - - +
676B TYR* 1.3 76.4 - - - +
678B TRP* 1.3 69.5 + - - +
679B SER 3.4 2.0 - - - -
680B SER* 2.7 23.8 + - - -
681B LEU* 3.2 4.1 + - - +
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Residues in contact with TRP 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.7 18.6 - - + -
23B ALA* 3.5 28.2 + - - +
24B PHE* 3.1 55.4 - + + -
27B GLU* 2.9 23.2 + - + +
28B LYS* 4.2 8.0 - - - +
629B PRO* 4.3 18.6 - - + -
677B GLY* 1.3 69.1 - - - -
679B SER* 1.3 66.4 + - - +
681B LEU* 2.5 44.9 + - + +
682B VAL* 3.1 24.0 + - + +
687B ILE* 3.5 34.1 - - + -
689B TYR* 3.2 22.5 + - - -
743B ILE* 5.0 5.6 - - + -
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Residues in contact with SER 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 2.4 52.0 + - - -
28B LYS* 5.6 2.4 - - - -
677B GLY 3.1 0.6 + - - -
678B TRP* 1.3 77.9 - - - +
680B SER* 1.3 57.8 + - - +
682B VAL* 3.4 4.6 + - - +
683B THR* 3.0 37.2 + - - +
689B TYR* 5.6 1.0 + - - -
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Residues in contact with SER 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B VAL* 4.5 4.2 + - - +
676B TYR* 3.8 33.2 + - - -
677B GLY 2.7 25.3 + - - -
679B SER* 1.3 71.2 - - - +
681B LEU* 1.3 64.5 + - - -
683B THR* 3.5 7.4 + - - -
684B SER* 2.8 27.3 + - - -
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Residues in contact with LEU 681 (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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20B VAL* 4.0 21.8 - - + -
23B ALA* 5.1 4.5 - - + -
647B ILE* 5.1 2.7 - - + -
651B HIS* 4.7 17.7 - - + -
655B ILE* 4.4 31.4 - - + -
676B TYR* 4.9 5.6 - - + +
677B GLY 3.2 4.4 + - - +
678B TRP* 2.5 28.6 + - + +
680B SER* 1.3 70.2 - - - +
682B VAL* 1.3 67.5 + - - +
684B SER* 2.2 27.6 + - - +
685B GLY 3.3 2.8 + - - -
686B VAL* 3.7 23.6 + - + -
687B ILE* 3.7 27.4 - - + -
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Residues in contact with VAL 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B ARG 5.7 1.5 - - - +
598B ARG* 3.9 7.8 - - - +
604B PRO* 4.2 15.5 - - + +
678B TRP* 3.1 29.5 + - + +
679B SER* 3.8 7.4 - - - +
680B SER 3.3 0.2 - - - -
681B LEU* 1.3 82.3 - - - +
683B THR* 1.3 62.2 + - + +
684B SER 2.9 3.5 + - - -
685B GLY* 3.3 8.0 + - - -
687B ILE* 3.6 31.5 - - + +
688B GLU* 5.1 0.9 - - - -
689B TYR* 3.1 51.4 - - + +
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Residues in contact with THR 683 (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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597B ARG 6.1 0.2 - - - -
598B ARG 3.4 12.6 - - - +
599B SER* 3.6 13.3 - - - +
600B GLY* 4.8 13.7 - - - +
604B PRO* 4.3 23.3 - - + -
679B SER* 3.0 21.8 + - - +
680B SER* 3.5 9.5 + - - -
682B VAL* 1.3 76.5 - - + +
684B SER* 1.3 62.2 + - - +
685B GLY 3.5 0.2 - - - -
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Residues in contact with SER 684 (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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598B ARG 4.3 1.0 - - - +
599B SER* 5.7 1.0 - - - -
651B HIS* 5.1 2.8 - - - -
676B TYR* 4.1 16.4 + - - -
680B SER 2.8 16.6 + - - -
681B LEU* 2.2 40.9 + - - +
683B THR* 1.3 75.3 - - - +
685B GLY* 1.3 56.7 + - - +
686B VAL* 4.0 13.0 - - - +
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Residues in contact with GLY 685 (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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598B ARG* 4.0 18.8 - - - -
632B ILE* 3.2 18.5 - - - +
646B ARG* 3.4 30.0 + - - -
681B LEU 3.3 1.6 + - - -
682B VAL 3.3 4.5 + - - -
683B THR 3.5 0.2 - - - -
684B SER* 1.3 79.4 + - - +
686B VAL* 1.3 64.4 + - - +
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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