Contacts of the strand formed by residues 646 - 653 (chain A) in PDB entry 1M10
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 VAL 646 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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606A PHE* 3.5 46.9 - - + -
616A ARG* 3.8 19.1 - - + +
618A ALA* 4.4 11.2 - - + +
641A LEU* 3.1 31.4 + - + +
642A LYS* 3.7 19.3 + - - +
644A LYS* 3.7 15.7 - - + +
645A LYS* 1.3 77.4 - - - +
647A ILE* 1.3 71.5 + - - +
648A VAL* 3.9 6.9 + - + +
672A ASN* 4.8 2.3 + - - +
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Residues in contact with ILE 647 (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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615A SER* 5.1 9.9 - - - +
616A ARG 2.9 17.9 + - - +
617A ILE* 3.0 11.8 - - + +
618A ALA 2.8 26.0 + - - -
645A LYS 4.4 6.7 - - - +
646A VAL* 1.3 75.8 - - - +
648A VAL* 1.3 64.4 + - - +
649A ILE* 4.0 9.2 - - + -
671A GLU* 3.2 58.6 - - + +
672A ASN* 3.7 4.9 - - - +
697A LEU* 4.2 25.6 - - + +
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Residues in contact with VAL 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A LEU* 5.1 6.3 - - + -
618A ALA* 3.7 22.7 - - + +
620A LEU* 4.5 11.7 - - + -
638A VAL* 5.2 7.9 - - + +
641A LEU* 4.1 27.1 - - + -
642A LYS 6.0 0.2 - - - +
646A VAL* 3.9 8.5 + - + +
647A ILE* 1.3 74.6 - - - +
649A ILE* 1.3 62.8 + - - +
650A PRO* 3.0 14.6 - - + +
665A ILE* 3.9 25.8 - - + -
672A ASN* 3.3 42.1 + - - +
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Residues in contact with ILE 649 (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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617A ILE* 3.5 17.5 - - + -
618A ALA 3.4 7.2 + - - -
619A LEU* 3.5 17.4 - - + +
620A LEU 3.4 17.3 + - - -
647A ILE* 3.9 3.7 + - + -
648A VAL* 1.3 73.2 - - - +
650A PRO* 1.3 62.9 - - - +
651A VAL* 3.4 7.6 - - + +
671A GLU 4.3 5.8 - - - +
673A LYS 3.5 15.9 - - - +
675A PHE* 3.8 22.0 - - + -
690A ILE* 5.7 3.8 - - + -
693A TYR* 3.7 28.0 - - + -
694A LEU* 3.4 33.7 - - + -
697A LEU* 4.2 4.7 - - + -
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Residues in contact with PRO 650 (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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620A LEU* 3.6 12.6 - - + +
622A MET* 4.0 18.2 - - - -
648A VAL* 3.0 16.1 - - + +
649A ILE* 1.3 84.0 - - - +
651A VAL* 1.3 60.2 + - - +
652A GLY 3.8 1.3 - - - -
662A ILE* 3.8 20.4 - - + -
665A ILE* 3.3 42.0 - - + -
672A ASN 4.5 0.2 - - - +
673A LYS 4.0 6.2 - - - +
674A ALA* 3.5 8.8 - - + +
675A PHE 3.2 20.1 + - - +
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Residues in contact with VAL 651 (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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536A PHE* 5.8 0.7 - - + -
619A LEU* 3.5 21.1 - - + -
620A LEU 2.9 11.4 + - - +
621A LEU* 4.0 18.8 - - + -
622A MET* 3.7 8.1 + - - -
649A ILE* 3.4 18.6 - - + +
650A PRO* 1.3 76.8 - - - +
652A GLY* 1.3 68.4 + - - +
653A ILE* 3.1 18.0 - - + +
675A PHE* 3.2 22.9 - - + +
677A LEU* 4.3 11.7 - - + -
683A LEU* 4.8 6.3 - - + -
690A ILE* 4.3 14.6 - - + -
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Residues in contact with GLY 652 (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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622A MET* 3.6 7.6 - - - -
650A PRO 3.8 0.8 + - - -
651A VAL* 1.3 76.1 - - - +
653A ILE* 1.3 65.5 + - - +
657A ALA* 3.8 4.9 - - - -
662A ILE* 3.5 29.8 - - - +
675A PHE 2.8 11.2 + - - +
676A VAL* 4.4 6.7 - - - -
677A LEU* 3.1 23.0 + - - +
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Residues in contact with ILE 653 (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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525A LEU* 5.1 8.0 - - + +
533A LEU* 4.4 11.9 - - + -
621A LEU* 4.4 17.9 - - + -
622A MET 3.0 13.9 + - - +
623A ALA* 3.4 29.0 - - + +
651A VAL* 3.1 17.7 - - + +
652A GLY* 1.3 83.0 - - - +
654A GLY* 1.3 72.1 + - - +
657A ALA* 3.5 5.3 - - - +
676A VAL* 6.2 0.2 - - - -
677A LEU* 3.2 10.5 - - + +
679A SER* 3.5 31.9 - - - +
680A VAL* 3.7 14.1 - - + +
683A LEU* 4.4 19.1 - - + -
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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