Contacts of the helix formed by residues 632 - 644 (chain A) in PDB entry 5OF4
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 SER 632 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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630A GLY* 3.3 8.1 + - - -
631A GLY* 1.3 76.5 - - - +
633A ARG* 1.3 53.0 + - - +
634A ARG 3.3 2.2 - - - -
635A GLN* 3.0 38.6 + - - +
636A GLU* 2.7 47.4 + - - +
639A ARG* 4.6 7.3 + - - -
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Residues in contact with ARG 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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631A GLY* 3.4 31.1 + - - -
632A SER* 1.3 77.4 - - - +
634A ARG* 1.3 59.0 + - + +
636A GLU* 3.3 12.2 + - - +
637A ALA 3.0 22.3 + - - -
672A TYR* 3.3 35.5 - - + +
675A LYS* 5.6 7.1 - - + +
676A ARG* 5.7 1.8 - - - -
679A PHE* 3.3 44.9 - - + -
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Residues in contact with ARG 634 (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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469A THR* 5.5 5.8 - - + -
471A VAL* 4.0 21.6 + - - +
472A ARG* 3.9 5.2 - - - +
473A GLU* 3.3 31.3 - - - +
474A ASP* 4.5 16.4 + - - +
632A SER 3.3 0.2 - - - -
633A ARG* 1.3 74.0 - - + +
635A GLN* 1.3 65.2 + - + +
637A ALA* 3.2 5.1 + - - +
638A GLN* 3.0 38.6 + - - +
679A PHE* 3.5 28.1 - - + -
683A GLN* 4.5 6.9 - - - +
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Residues in contact with GLN 635 (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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445A THR* 5.6 11.7 - - + +
632A SER* 3.0 31.2 + - - +
634A ARG* 1.3 77.1 - - + +
636A GLU* 1.3 57.7 + - - +
638A GLN* 3.3 8.5 + - - +
639A ARG* 2.9 54.0 + - + +
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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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625A GLN* 3.8 18.0 + - - +
627A SER* 3.7 11.6 + - - +
630A GLY* 3.5 16.1 + - - +
632A SER* 2.7 33.4 + - - +
633A ARG* 3.4 11.0 - - - +
635A GLN* 1.3 70.7 - - - +
637A ALA* 1.3 65.4 + - - +
639A ARG* 3.3 15.9 + - - +
640A LEU* 3.0 31.5 + - + +
672A TYR* 2.4 30.3 + - - -
676A ARG* 2.8 26.0 + - - +
679A PHE* 6.1 0.2 - - - -
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Residues in contact with ALA 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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342A CYS* 4.9 1.5 - - - -
633A ARG 3.0 13.6 + - - +
634A ARG* 3.2 11.0 + - - +
636A GLU* 1.3 78.0 - - - +
638A GLN* 1.3 61.0 + - + +
640A LEU* 3.3 16.7 - - - +
641A GLY* 2.9 24.8 + - - -
679A PHE* 4.4 2.7 - - + -
680A LEU* 5.2 4.0 - - + -
683A GLN* 3.5 27.4 - - - +
685A TYR* 3.9 13.6 + - + +
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Residues in contact with GLN 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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342A CYS* 3.7 26.0 - - - +
442A GLU* 3.5 8.3 - - - +
444A HIS* 3.2 30.4 + - - -
445A THR* 5.4 0.3 - - - +
468A ALA* 5.6 1.1 - - - -
469A THR* 2.4 36.1 + - - +
634A ARG* 3.0 24.9 + - - +
635A GLN* 3.9 6.3 - - - +
637A ALA* 1.3 76.0 - - + +
639A ARG* 1.3 61.8 + - - +
641A GLY* 3.3 0.9 + - - -
642A ARG* 2.9 44.7 + - - +
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Residues in contact with ARG 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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561A PHE* 4.0 26.9 - - - -
609A LYS 5.4 6.3 + - - -
612A ASP* 4.0 33.7 - - + +
613A THR* 3.6 21.6 + - - -
623A LEU* 5.0 3.4 - - + -
625A GLN* 5.7 2.3 - - - +
632A SER* 4.6 11.7 + - - -
635A GLN* 2.9 39.4 + - - +
636A GLU* 3.6 15.8 - - - +
637A ALA 3.3 0.2 - - - -
638A GLN* 1.3 77.0 - - - +
640A LEU* 1.3 58.5 + - - +
642A ARG* 3.3 4.2 + - - +
643A VAL* 2.9 39.9 + - + +
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Residues in contact with LEU 640 (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 CYS* 4.5 12.8 - - - -
623A LEU* 3.8 26.4 - - + +
625A GLN* 5.0 3.4 - - - +
636A GLU* 3.0 23.6 + - + +
637A ALA* 3.3 19.1 - - - +
639A ARG* 1.3 76.9 - - - +
641A GLY* 1.3 63.0 + - - +
643A VAL* 4.5 0.4 - - - -
644A LEU* 3.4 35.1 + - + +
659A PHE* 4.3 27.4 - - + -
676A ARG* 5.0 3.8 - - - +
680A LEU* 4.6 16.2 - - + -
685A TYR* 3.8 32.5 - - + -
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Residues in contact with GLY 641 (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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342A CYS* 3.6 28.6 - - - +
343A GLY* 4.8 1.2 - - - -
637A ALA 2.9 16.0 + - - -
638A GLN 3.3 3.6 + - - -
639A ARG 3.2 0.4 - - - -
640A LEU* 1.3 82.2 - - - +
642A ARG* 1.3 61.2 + - - +
643A VAL 3.5 0.3 + - - -
644A LEU* 3.8 15.0 + - - +
685A TYR* 5.1 4.9 - - - -
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Residues in contact with ARG 642 (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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342A CYS* 4.4 3.2 - - + +
343A GLY* 4.1 14.6 - - - +
346A LYS* 3.1 34.1 - - - +
366A ASN* 5.7 1.8 - - - +
373A GLN* 6.1 1.1 - - - -
442A GLU* 2.5 42.8 + - - +
612A ASP 5.9 0.4 + - - -
618A PRO* 3.7 9.2 - - + +
619A GLU* 5.4 0.3 - - - +
638A GLN* 2.9 27.4 + - - +
639A ARG* 4.2 3.4 - - - +
641A GLY* 1.3 73.5 - - - +
643A VAL* 1.3 68.2 + - + +
644A LEU 4.9 0.4 - - - -
645A ARG* 4.1 12.8 - - - +
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Residues in contact with VAL 643 (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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559A ILE* 3.8 33.4 - - + -
607A ILE* 5.9 0.7 - - + -
612A ASP* 5.0 3.8 - - - +
618A PRO* 3.4 38.5 - - + +
620A ALA* 3.3 23.4 + - + +
623A LEU* 4.1 21.1 - - + -
639A ARG* 2.9 27.6 + - + +
640A LEU* 4.5 4.5 - - - +
642A ARG* 1.3 81.3 - - + +
644A LEU* 1.3 55.5 + - + +
645A ARG* 2.8 19.2 + - - +
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Residues in contact with LEU 644 (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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503A ALA* 3.5 12.5 - - - +
505A VAL* 3.8 36.8 - - + -
620A ALA 4.1 1.1 - - - -
621A ASN 3.5 20.2 - - - +
622A VAL 3.9 0.4 - - - -
623A LEU* 3.4 24.5 - - + +
640A LEU* 3.4 29.7 + - + +
641A GLY 3.8 11.3 + - - +
642A ARG 3.5 0.6 - - - -
643A VAL* 1.3 72.4 - - + +
645A ARG* 1.3 65.0 + - - +
657A ALA* 4.0 10.1 - - + -
658A PHE 3.4 24.5 - - - +
659A PHE* 4.2 12.1 - - + -
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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