Contacts of the strand formed by residues 626 - 633 (chain A) in PDB entry 1M7X
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 PHE 626 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511A ILE* 3.8 25.6 - - + -
515A TYR* 3.8 18.0 + - - +
560A PHE* 4.5 0.9 - + - -
561A PRO* 3.3 31.0 - - + -
622A ASP 4.1 0.4 + - - -
623A PRO* 2.8 23.0 + - - +
624A TYR 3.3 0.6 - - - -
625A GLY* 1.3 80.7 - - - +
627A GLU* 1.3 86.2 + - - +
628A TRP* 3.6 42.2 - + - -
641A PHE* 3.3 58.8 - + + -
642A VAL* 3.6 4.5 - - - -
643A ARG* 4.3 2.7 - - - -
644A ARG* 4.6 2.1 + - - -
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Residues in contact with GLU 627 (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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626A PHE* 1.3 86.9 - - - +
628A TRP* 1.3 68.7 + - - +
629A LEU* 4.6 0.8 - - - +
641A PHE* 3.3 1.7 - - - +
642A VAL* 2.8 36.6 + - + +
644A ARG* 3.1 27.3 + - - +
670A ASN* 3.2 26.3 + - - +
707A ARG* 2.9 22.6 + - - +
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Residues in contact with TRP 628 (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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507A LEU 4.4 1.3 - - - -
508A THR* 4.0 28.5 + - + -
511A ILE* 3.7 27.2 - - + +
556A TRP* 4.0 24.5 - + - -
560A PHE* 4.8 0.2 - + - -
626A PHE* 3.6 26.6 - + - -
627A GLU* 1.3 78.7 - - - +
629A LEU* 1.3 60.9 + - - +
630A VAL 4.0 8.1 - - - +
631A VAL* 3.5 37.9 - - + +
639A LEU* 4.3 14.4 - - + -
640A ILE 3.4 19.1 - - - -
641A PHE* 3.6 22.4 - + + -
707A ARG* 3.0 21.5 + - - -
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Residues in contact with LEU 629 (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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627A GLU* 4.6 1.3 - - - +
628A TRP* 1.3 76.2 - - - +
630A VAL* 1.3 70.5 + - + +
631A VAL 4.2 0.2 - - - -
640A ILE* 2.9 26.3 + - + +
641A PHE* 4.2 12.1 - - - -
642A VAL* 4.1 22.2 - - + +
652A ILE* 4.4 5.8 - - + -
667A PHE* 4.1 16.6 - - + -
668A GLY 3.4 25.1 - - - +
669A ILE* 4.3 9.0 - - + -
670A ASN* 4.1 17.3 - - - +
705A HIS* 3.9 13.5 + - - +
707A ARG* 3.7 37.9 + - - +
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Residues in contact with VAL 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A TRP* 4.0 2.0 - - - -
629A LEU* 1.3 83.7 - - - +
631A VAL* 1.3 58.2 + - - +
632A ASP* 4.2 3.6 - - - +
633A ASP* 3.8 23.6 - - + +
638A VAL 4.2 3.8 - - - +
639A LEU* 3.6 7.6 - - - -
640A ILE* 2.9 45.2 + - + +
665A TYR* 3.8 19.5 - - - +
667A PHE* 3.6 29.6 - - + -
705A HIS* 3.7 24.0 - - + +
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Residues in contact with VAL 631 (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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504A HIS* 2.9 25.7 + - - -
508A THR* 3.9 19.8 - - + +
628A TRP* 3.5 51.5 - - + +
629A LEU 4.2 0.6 - - - -
630A VAL* 1.3 73.7 - - - +
632A ASP* 1.3 70.5 + - + +
633A ASP 3.8 0.2 - - - -
634A LYS* 5.3 1.0 - - - -
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Residues in contact with ASP 632 (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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504A HIS* 4.1 1.8 - - - -
630A VAL* 4.2 8.1 - - - +
631A VAL* 1.3 89.7 + - + +
633A ASP* 1.3 57.0 + - - +
634A LYS* 2.9 27.7 + - - +
635A GLU* 4.1 6.4 - - - +
705A HIS* 4.7 9.0 + - - -
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Residues in contact with ASP 633 (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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504A HIS* 3.3 9.0 + - - -
630A VAL* 3.8 9.3 - - + +
631A VAL 3.8 1.8 - - - -
632A ASP* 1.3 75.4 + - - +
634A LYS* 1.3 54.6 + - - +
635A GLU* 2.7 25.9 - - - +
636A ARG* 2.7 45.3 + - - +
637A SER 3.1 16.8 + - - -
638A VAL* 3.3 23.0 + - - +
665A TYR* 2.6 30.2 + - - +
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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