Contacts of the strand formed by residues 635 - 639 (chain A) in PDB entry 1HMU
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 ILE 635 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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630A LEU 4.0 0.2 - - - +
631A SER* 3.4 3.3 - - - -
632A VAL* 2.9 44.8 + - + +
633A ALA* 4.3 7.4 - - + +
634A GLY* 1.3 83.6 - - - +
636A GLU* 1.3 59.3 + - - +
637A ILE* 4.3 18.8 - - + -
647A ILE* 6.0 0.7 - - + -
650A ILE* 4.6 15.7 - - + +
654A GLN* 3.5 28.7 - - - +
672A ILE* 4.0 21.1 - - + -
673A ARG 3.2 11.9 - - - +
674A ASP* 4.5 12.6 - - + +
675A LEU* 3.2 8.5 - - - +
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Residues in contact with GLU 636 (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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629A LYS* 3.1 51.1 + - + +
630A LEU 3.2 10.8 - - - +
631A SER* 3.9 14.5 + - - +
635A ILE* 1.3 74.0 - - - +
637A ILE* 1.3 62.4 + - - +
638A GLU* 4.6 6.4 - - + +
671A SER 3.4 4.3 - - - +
672A ILE* 3.5 0.8 - - - -
673A ARG* 2.7 64.9 + - + +
675A LEU* 3.9 13.0 - - + -
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Residues in contact with ILE 637 (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 VAL* 4.4 14.8 - - + -
624A PHE* 4.5 12.8 - - + -
628A GLY 4.1 0.3 - - - +
629A LYS* 3.2 3.2 - - - +
630A LEU* 2.7 51.6 + - + +
632A VAL* 4.2 21.1 - - + -
635A ILE* 4.3 14.8 - - + -
636A GLU* 1.3 74.6 - - - +
638A GLU* 1.3 62.2 - - - +
645A VAL* 5.4 2.9 - - + -
647A ILE* 3.5 28.3 - - + -
650A ILE* 5.8 0.9 - - + -
670A LEU* 4.3 19.7 - - + -
671A SER 3.4 4.3 - - - +
672A ILE* 3.6 26.2 - - + -
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Residues in contact with GLU 638 (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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624A PHE* 5.4 0.2 - - - -
628A GLY* 3.4 17.3 - - - +
629A LYS* 3.7 28.7 + - + -
636A GLU* 4.6 7.0 - - - +
637A ILE* 1.3 76.3 - - - +
639A THR* 1.3 71.5 + - - +
640A ASP* 5.7 2.4 - - - +
669A VAL 3.6 0.7 - - - +
670A LEU* 3.2 9.4 - - - +
671A SER* 2.8 48.6 + - - +
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Residues in contact with THR 639 (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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624A PHE* 3.6 39.0 - - + -
627A ALA* 3.5 1.6 - - - +
628A GLY 3.1 25.2 + - - +
638A GLU* 1.3 81.8 - - - +
640A ASP* 1.3 60.5 + - - +
641A LYS* 2.9 29.2 + - - +
643A CYS* 3.6 9.2 - - - -
668A ALA* 4.5 5.2 - - - +
669A VAL 3.4 8.4 + - - -
670A LEU* 3.6 18.0 - - - +
685A ILE* 5.3 0.7 - - - +
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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