Contacts of the helix formed by residues 671 - 676 (chain A) in PDB entry 5M5X
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 GLN 671 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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670A ILE* 1.3 92.5 - - + +
672A ASP* 1.3 67.5 + - - +
673A HIS 3.6 1.1 - - - -
674A ILE* 3.2 4.6 - - - +
675A SER* 2.8 30.3 + - - -
933A ALA* 3.5 17.3 - - + +
934A LYS* 3.1 48.8 - - + +
783B MET* 6.0 1.3 - - + -
784B ASP* 3.1 35.7 + - + +
952B HIS* 3.1 35.0 + - + +
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Residues in contact with ASP 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A TYR* 5.0 3.7 - - + -
670A ILE* 5.2 1.0 - - - +
671A GLN* 1.3 76.5 - - - +
673A HIS* 1.3 76.9 + - + +
674A ILE 3.2 0.3 + - - -
675A SER* 3.2 4.0 + - - -
676A ALA 3.1 18.7 + - - -
821A ILE* 3.7 20.1 - - + +
777B SER* 4.5 10.3 - - - -
780B GLY* 4.0 12.9 - - - +
782B ASP 3.2 12.0 - - - +
783B MET* 3.1 32.4 - - + +
784B ASP 5.5 0.2 + - - -
950B ASN* 5.0 3.8 - - - +
951B PRO* 5.9 0.3 - - - +
952B HIS* 3.0 29.7 + - - +
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Residues in contact with HIS 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A PRO* 5.3 2.7 - - + -
617A HIS* 5.5 2.9 - - - -
618A TYR* 3.5 33.6 - + - -
669A LEU* 3.2 39.1 - - + +
672A ASP* 1.3 86.9 - - + +
674A ILE* 1.3 58.2 + - - +
676A ALA* 4.1 1.6 - - - -
677A GLY 3.7 1.9 + - - -
786A TYR* 5.2 2.0 - - - -
814A GLY* 3.0 24.3 + - - -
817A PHE* 3.1 49.5 - - + -
818A THR* 2.6 38.1 + - - +
821A ILE* 4.7 2.9 - - + -
780B GLY* 5.4 3.2 + - - -
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Residues in contact with ILE 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669A LEU* 4.7 10.3 - - + +
670A ILE 3.1 27.6 - - - +
671A GLN* 3.2 10.3 - - - +
673A HIS* 1.3 77.8 - - - +
675A SER* 1.3 66.6 + - - +
676A ALA 3.1 1.6 - - - -
677A GLY* 3.1 11.9 + - - +
678A VAL* 3.6 14.2 + - - +
781A LEU 5.2 1.6 - - - +
782A ASP* 3.9 13.7 - - - +
783A LYS* 3.4 47.6 - - + +
786A TYR* 4.3 12.1 - - + +
931A SER* 3.6 17.7 - - - +
932A GLY 4.2 3.6 - - - +
933A ALA* 3.8 9.2 - - + -
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Residues in contact with SER 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A GLN 2.8 23.8 + - - -
672A ASP 3.2 2.0 + - - -
674A ILE* 1.3 76.7 - - - +
676A ALA* 1.3 58.6 + - - +
678A VAL* 4.1 10.6 + - - +
679A TRP* 3.3 24.8 + - - -
826A PHE* 4.0 20.2 - - - -
927A ALA 6.0 1.8 - - - -
928A MET* 4.2 8.3 - - - +
931A SER* 5.8 1.3 - - - -
933A ALA* 3.5 17.4 - - - +
952B HIS* 3.3 24.1 + - - -
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Residues in contact with ALA 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A ASP 3.1 10.9 + - - +
674A ILE 3.1 1.0 - - - -
675A SER* 1.3 75.6 - - - +
677A GLY* 1.3 59.8 + - - +
678A VAL 3.4 0.2 - - - -
679A TRP* 3.5 4.8 + - - +
680A LEU* 2.8 31.0 + - - +
817A PHE* 4.0 17.0 - - + -
820A TYR* 3.8 20.1 - - + -
821A ILE* 3.7 30.5 - - + -
826A PHE* 5.6 3.3 - - + +
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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