Contacts of the strand formed by residues 640 - 647 (chain E) in PDB entry 4WEB
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 640 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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636E TYR* 3.5 2.8 - - - -
637E VAL 2.9 39.6 + - - +
638E GLY 3.3 3.5 - - - +
639E GLY* 1.3 79.9 - - - +
641E GLU* 1.3 73.9 - - - +
642E HIS* 3.4 19.7 - - - +
1H GLU* 4.0 21.1 - - - +
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Residues in contact with GLU 641 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634E ARG* 2.9 15.6 + - + -
635E MET 3.5 4.9 - - - +
636E TYR* 3.4 32.2 + - + -
639E GLY 4.1 0.6 + - - -
640E VAL* 1.3 80.9 - - - +
642E HIS* 1.3 72.6 + - - +
643E ARG* 2.8 32.2 + - - +
703E ARF 2.6 33.1 + - - -
1H GLU* 5.1 4.9 + - - +
2H VAL* 3.6 27.3 - - + +
26H GLY 4.6 11.1 - - - +
27H PHE* 5.7 0.3 - - - +
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Residues in contact with HIS 642 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512E THR* 3.4 34.9 + - - -
513E PRO* 3.5 18.8 - - + +
514E SER* 2.9 27.2 + - - +
634E ARG* 3.4 4.7 - - - -
635E MET* 2.6 42.6 + - + +
637E VAL* 4.0 14.2 - - + +
640E VAL* 3.4 34.2 - - + +
641E GLU* 1.3 77.1 - - - +
643E ARG* 1.3 64.5 + - - +
644E LEU* 4.0 5.0 + - + -
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Residues in contact with ARG 643 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514E SER* 4.3 4.5 + - - -
515E PRO* 5.7 0.5 - - - +
633E ILE 3.7 9.0 - - - -
634E ARG* 3.7 14.8 - - - +
641E GLU* 2.8 28.7 + - - -
642E HIS* 1.3 79.6 - - - +
644E LEU* 1.3 67.3 + - - +
2H VAL* 4.0 10.0 - - + +
27H PHE* 3.9 40.2 - - + +
28H ASN 4.9 1.1 + - - +
31H ASP* 3.4 30.3 + - + +
32H THR* 3.5 23.6 - - + +
98H THR* 3.5 7.7 + - - -
99H SER 3.8 12.5 + - - -
100H ASP* 3.9 2.4 - - - +
106H ASP* 2.4 46.0 + - - -
107H SER* 4.0 3.6 + - - -
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Residues in contact with LEU 644 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513E PRO* 3.7 32.3 - - + +
514E SER* 3.4 42.8 - - - +
515E PRO* 4.0 8.3 - - + -
607E LEU* 4.9 0.9 - - + -
613E ILE* 4.3 18.6 - - + -
632E LYS* 3.6 2.6 - - - -
633E ILE* 2.7 58.8 + - + +
635E MET* 4.4 11.9 - - + -
642E HIS* 4.3 7.2 - - + +
643E ARG* 1.3 79.3 - - - +
645E THR* 1.3 65.8 + - - +
646E ALA* 6.0 0.2 - - + -
31H ASP* 3.6 10.2 - - - +
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Residues in contact with THR 645 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613E ILE* 3.7 6.6 - - - +
614E ASP* 2.7 53.1 + - + +
630E ILE* 4.1 21.1 - - + -
631E PHE 3.3 15.9 - - - +
632E LYS* 4.4 11.8 + - + +
644E LEU* 1.3 76.4 + - - +
646E ALA* 1.3 58.3 + - - +
30H LYS 4.5 2.8 + - - -
31H ASP* 2.6 33.6 + - - -
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Residues in contact with ALA 646 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607E LEU* 4.0 23.3 - - + -
611E CYS* 5.0 6.1 - - + -
612E LEU 3.6 10.5 - - - +
614E ASP* 4.7 0.2 - - - -
629E THR 3.6 1.2 - - - +
630E ILE* 3.2 4.3 - - - -
631E PHE* 2.6 49.0 + - + +
633E ILE* 4.1 15.7 - - + -
644E LEU 4.1 0.4 + - - -
645E THR* 1.3 75.0 - - - +
647E ALA* 1.3 61.6 + - - +
648E CYS* 4.0 5.3 + - - -
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Residues in contact with ALA 647 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611E CYS* 3.3 1.7 - - - -
612E LEU* 3.1 33.3 + - + +
614E ASP* 4.6 1.8 - - + +
618E ARG* 3.5 42.8 - - - +
628E TYR* 3.5 18.4 - - + -
629E THR 3.2 5.6 - - - -
630E ILE* 3.9 9.9 - - + -
646E ALA* 1.3 72.1 - - - +
648E CYS* 1.3 62.4 + - - +
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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