Contacts of the helix formed by residues 635 - 650 (chain A) in PDB entry 4FYT
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 ASP 635 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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553A THR* 5.5 0.2 - - - +
554A VAL 3.0 9.5 + - - +
555A ASP* 4.3 15.0 - - - +
556A THR* 2.7 47.1 + - - +
557A SER* 4.9 3.8 + - - -
634A TYR* 1.3 76.2 - - - +
636A GLU* 1.3 63.9 + - - +
637A GLU* 3.3 13.7 + - - +
638A ASN* 3.0 26.6 + - - +
639A TRP* 3.1 16.8 + - - -
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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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634A TYR 5.0 1.1 - - - +
635A ASP* 1.3 75.7 - - - +
637A GLU* 1.3 56.9 + - - +
639A TRP* 3.3 9.1 + - + +
640A ARG* 2.9 51.7 + - + +
673A LYS 5.7 0.3 - - - +
674A VAL* 5.3 2.0 - - + -
675A PRO* 3.6 27.7 - - + +
678A LEU* 4.0 16.8 - - + +
1E NAG 4.2 20.1 - - - +
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Residues in contact with GLU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A THR* 5.5 1.0 + - - +
557A SER* 4.8 9.2 + - - -
616A GLY 5.0 1.9 - - - +
635A ASP* 3.2 11.1 + - - +
636A GLU* 1.3 78.8 - - - +
638A ASN* 1.3 62.1 + - - +
640A ARG* 3.2 27.8 + - + +
641A LYS* 3.1 47.1 + - + +
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Residues in contact with ASN 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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556A THR* 3.7 20.8 + - + +
614A THR* 4.6 1.2 + - - +
618A GLU 4.4 0.7 - - - +
619A TRP* 3.5 11.5 - - - +
620A VAL* 2.9 41.4 + - - +
634A TYR* 3.4 25.4 - - + -
635A ASP* 3.0 28.8 + - - +
637A GLU* 1.3 72.9 - - - +
639A TRP* 1.3 67.1 + - - +
641A LYS* 3.2 11.8 + - - +
642A ILE* 3.0 37.8 + - - +
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Residues in contact with TRP 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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632A VAL 4.0 13.5 - - - -
633A ASN* 2.8 28.8 + - - -
634A TYR* 3.2 48.7 + + + +
635A ASP 3.1 15.1 + - - -
636A GLU* 3.5 10.3 - - + +
638A ASN* 1.3 75.8 - - - +
640A ARG* 1.3 59.3 + - + +
642A ILE* 3.2 18.1 + - + +
643A GLN* 2.9 34.5 + - - +
661A ILE* 4.0 22.2 - - + -
664A ASP* 5.0 1.8 - - + -
665A ALA* 4.2 19.3 - - + -
668A LEU* 4.0 8.3 - - + -
674A VAL* 3.9 5.3 - - + +
678A LEU* 3.7 35.4 - - + -
682A ASN* 3.6 26.2 - - - -
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Residues in contact with ARG 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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636A GLU* 2.9 44.8 + - + +
637A GLU* 3.2 31.4 + - + +
639A TRP* 1.3 76.4 - - + +
641A LYS* 1.3 57.6 - - - +
643A GLN* 3.3 18.2 + - - +
644A THR* 2.9 32.5 + - - +
678A LEU* 6.2 1.6 - - + -
1E NAG 5.1 12.2 + - - +
2E NAG 5.9 6.5 - - - -
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Residues in contact with LYS 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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556A THR* 5.4 1.0 + - - -
614A THR* 3.5 18.0 + - - -
615A SER* 4.6 3.8 - - - +
616A GLY 3.1 25.4 + - - +
617A ASN* 4.0 8.3 - - - +
618A GLU 2.7 32.8 + - - +
619A TRP* 4.0 17.2 - - + -
637A GLU* 3.1 44.0 + - + +
638A ASN* 3.2 15.2 + - - +
640A ARG* 1.3 72.1 - - + +
642A ILE* 1.3 60.8 + - - +
644A THR* 3.4 8.8 + - - +
645A GLN* 2.9 27.7 + - - +
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Residues in contact with ILE 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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619A TRP* 4.6 12.1 - - + -
621A LEU* 3.4 28.5 - - + -
634A TYR* 3.8 16.8 - - + -
638A ASN* 3.0 37.6 + - - +
639A TRP* 3.2 19.3 + - + +
641A LYS* 1.3 75.9 - - - +
643A GLN* 1.3 57.5 + - + +
645A GLN* 3.2 8.6 + - - +
646A LEU* 2.9 31.7 + - + +
653A ILE* 4.4 5.6 - - + -
661A ILE* 3.6 39.5 - - + -
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Residues in contact with GLN 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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639A TRP* 2.9 20.8 + - - +
640A ARG* 3.3 21.6 + - - +
642A ILE* 1.3 75.7 - - + +
644A THR* 1.3 61.5 + - - +
646A LEU* 3.2 11.6 + - + +
647A GLN* 3.0 28.0 + - + +
678A LEU* 3.4 32.5 + - - +
681A ASN* 3.6 25.0 + - - +
682A ASN* 2.8 32.0 + - - +
1E NAG 5.1 3.6 - - - +
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Residues in contact with THR 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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640A ARG* 2.9 20.2 + - - +
641A LYS* 3.6 8.5 - - - +
642A ILE 3.2 0.2 - - - -
643A GLN* 1.3 75.2 - - - +
645A GLN* 1.3 60.4 + - - +
647A GLN* 3.1 8.0 + - + +
648A ARG* 2.8 50.5 + - + +
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Residues in contact with GLN 645 (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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619A TRP* 2.8 37.8 + - + +
641A LYS 2.9 14.4 + - - +
642A ILE* 3.2 9.8 + - - +
644A THR* 1.3 78.0 - - - +
646A LEU* 1.3 56.5 - - - +
648A ARG* 4.4 11.4 + - - +
649A ASP* 2.9 69.1 + - - +
652A ALA* 3.4 16.9 - - + +
653A ILE* 3.8 23.1 - - + -
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Residues in contact with LEU 646 (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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642A ILE* 2.9 24.0 + - + +
643A GLN* 3.6 14.4 - - + +
644A THR 3.2 0.4 - - - -
645A GLN* 1.3 75.5 - - - +
647A GLN* 1.3 62.3 + - - +
650A HIS* 3.5 39.8 + - + +
653A ILE* 3.9 19.3 - - + -
658A ARG* 4.1 10.8 - - + -
661A ILE* 4.2 24.9 - - + -
682A ASN* 4.5 9.2 - - - +
685A PHE* 3.8 53.2 - - + +
688A GLU* 4.6 2.9 - - - +
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Residues in contact with GLN 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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643A GLN* 3.0 16.8 + - + +
644A THR* 3.1 9.4 + - + +
646A LEU* 1.3 77.4 - - - +
648A ARG* 1.3 64.6 + - + +
681A ASN 5.7 0.2 + - - -
684A LEU* 4.2 14.3 - - - +
685A PHE* 3.9 32.3 - - - +
688A GLU* 4.3 15.5 + - - +
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Residues in contact with ARG 648 (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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644A THR* 2.8 43.7 + - + +
645A GLN* 4.0 12.7 + - - +
647A GLN* 1.3 77.2 - - + +
649A ASP* 1.3 64.3 + - + +
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Residues in contact with ASP 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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645A GLN* 2.9 31.2 + - - +
648A ARG* 1.3 79.6 - - + +
650A HIS* 1.3 63.7 + - - +
651A SER* 2.7 30.7 + - - -
652A ALA* 3.1 17.9 + - + +
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Residues in contact with HIS 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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645A GLN* 3.6 7.5 + - - -
646A LEU* 3.5 26.3 + - + +
649A ASP* 1.3 74.5 + - - +
651A SER* 1.3 65.5 + - - +
652A ALA 3.1 1.7 + - - -
653A ILE* 3.1 13.7 + - - +
658A ARG* 3.3 27.7 - - - -
685A PHE* 3.8 16.8 - + + -
688A GLU* 3.3 56.7 + - + +
689A GLU* 3.6 29.5 + - - -
690A ARG 5.1 0.6 + - - -
1023A SO4 3.9 10.1 + - - -
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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