Contacts of the strand formed by residues 637 - 643 (chain 3) in PDB entry 5Z58
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 PRO 637 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5883 VAL* 3.7 23.6 - - + +
5893 CYS* 4.7 7.0 - - - -
6093 LEU 5.4 0.2 - - - +
6123 ASN* 3.9 21.1 - - - +
6133 THR 5.0 4.5 - - - +
6333 LEU* 3.5 34.3 - - + -
6353 ALA 3.1 9.6 - - - +
6363 GLN* 1.3 95.5 - - + +
6383 GLU* 1.3 62.6 + - - +
6403 LEU* 4.6 8.3 - - + -
6673 ILE* 4.4 2.9 - - + -
6683 GLY 3.4 12.8 - - - +
6693 LEU* 3.4 9.6 - - + -
6703 GLN* 3.9 2.7 - - - +
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Residues in contact with GLU 638 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5883 VAL* 4.0 7.4 - - - +
5893 CYS* 3.1 19.3 - - - +
6373 PRO* 1.3 75.1 - - - +
6393 SER* 1.3 60.3 + - - +
6683 GLY 2.8 6.7 + - - -
6693 LEU* 3.1 26.4 - - - +
6703 GLN* 3.8 11.5 - - - +
6983 PRO* 3.3 22.9 - - + +
6993 VAL 3.1 28.7 - - - +
7003 LYS* 4.2 21.2 - - + +
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Residues in contact with SER 639 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5893 CYS* 3.5 11.2 - - - -
6373 PRO 3.9 0.2 - - - -
6383 GLU* 1.3 81.0 - - - +
6403 LEU* 1.3 65.0 + - - +
6683 GLY* 2.9 30.6 + - - +
6993 VAL 2.6 13.4 + - - -
7003 LYS* 3.1 6.0 - - - -
7013 LEU* 2.4 39.6 + - - +
7023 PHE* 5.9 2.9 - - - -
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Residues in contact with LEU 640 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5893 CYS* 3.7 25.2 - - - +
5903 MET 5.2 0.2 - - - -
5913 SER* 3.0 26.4 + - - +
6063 ALA* 4.1 23.6 - - + -
6083 GLY* 4.1 14.6 - - - +
6133 THR 5.6 0.2 - - - +
6143 VAL* 3.5 30.5 - - + -
6333 LEU* 4.5 6.5 - - + -
6373 PRO* 4.6 4.5 - - + -
6393 SER* 1.3 77.1 - - - +
6413 CYS* 1.3 61.7 + - - +
6653 LEU* 4.7 5.2 - - + -
6663 ASN 3.3 2.9 - - - +
6673 ILE* 3.5 45.3 - - + -
7013 LEU* 3.8 7.0 - - - +
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Residues in contact with CYS 641 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5913 SER* 4.3 5.8 - - - -
6403 LEU* 1.3 75.2 - - - +
6423 ILE* 1.3 75.6 + - - +
6653 LEU* 4.9 0.2 - - - -
6663 ASN* 2.9 47.5 + - + +
7013 LEU* 3.4 28.6 - - + +
7023 PHE* 3.8 23.1 - - - -
7033 ARG* 4.0 16.4 - - - -
7123 VAL* 4.7 15.0 - - + -
7133 LEU 5.3 0.2 - - - +
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Residues in contact with ILE 642 (chain 3).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5913 SER* 4.4 11.6 + - - +
5933 ALA* 4.0 31.9 - - + -
5943 ASN 5.7 0.4 - - - +
6043 PHE* 4.5 11.9 - - + -
6053 LEU 5.0 0.2 - - - -
6063 ALA* 4.1 24.5 - - + +
6163 ILE* 5.1 0.9 - - + -
6403 LEU 4.2 0.4 - - - -
6413 CYS* 1.3 81.2 - - - +
6433 VAL* 1.3 66.2 + - - +
6633 LEU* 5.3 9.4 - - + -
6643 TYR 3.5 9.0 - - - +
6653 LEU* 3.7 33.4 - - + +
6793 LEU* 5.2 12.1 - - + -
7033 ARG* 2.3 33.4 + - - +
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Residues in contact with VAL 643 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6413 CYS* 4.8 0.4 - - - -
6423 ILE* 1.3 82.0 - - - +
6443 GLU* 1.3 60.8 + - - +
6453 MET 3.3 25.1 - - - +
6623 PHE 3.3 0.3 - - - +
6633 LEU* 3.3 5.5 - - - +
6643 TYR* 2.8 55.0 + - + +
6663 ASN* 3.6 6.5 - - - +
7033 ARG* 3.4 20.6 - - + +
7103 GLU* 3.8 16.4 - - + +
7113 ALA 5.7 0.7 - - - -
7123 VAL* 3.5 34.1 - - + -
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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