Contacts of the strand formed by residues 197 - 202 (chain 4) in PDB entry 5KZ5
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 THR 197 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1424 TYR* 3.8 9.5 - - - -
1464 LYS* 3.9 3.7 + - - -
1484 HIS* 3.6 42.2 + - - +
1504 ILE* 3.8 11.7 - - + -
1924 ALA 3.8 1.2 + - - -
1944 GLN* 3.2 36.7 + - - +
1954 PRO 4.3 0.2 - - - +
1964 ASP* 1.4 78.5 - - - +
1984 SER* 1.4 61.7 + - - +
1994 LEU 3.4 23.1 - - - +
2264 LYS 3.9 1.0 - - - +
2274 VAL* 3.4 23.5 - - + +
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Residues in contact with SER 198 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1384 VAL* 3.3 22.7 - - - +
1394 ALA 3.3 24.2 + - - -
1424 TYR* 3.6 32.6 - - - +
1434 ARG* 3.7 10.6 + - - +
1464 LYS* 5.1 3.2 + - - +
1484 HIS 3.6 5.5 + - - -
1494 LEU* 3.6 18.5 - - - +
1964 ASP 3.5 0.6 + - - -
1974 THR* 1.4 74.9 - - - +
1994 LEU* 1.4 59.4 + - - +
2274 VAL* 3.8 4.7 - - - -
2284 TYR* 3.9 9.6 + - - +
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Residues in contact with LEU 199 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1354 ILE* 3.4 50.5 - - + +
1364 LYS* 4.9 4.3 - - - +
1384 VAL* 3.5 19.1 - - + -
1394 ALA* 4.4 5.4 - - + -
1484 HIS 4.4 0.2 + - - -
1494 LEU* 4.0 33.9 - - + -
1504 ILE* 3.2 41.8 + - - +
1514 THR* 4.6 4.5 - - + -
1974 THR* 3.4 11.0 - - - +
1984 SER* 1.4 81.1 + - - +
2004 VAL* 1.3 79.5 + - - +
2014 SER* 4.1 2.0 - - - +
2274 VAL* 3.6 3.5 - - - +
2284 TYR 3.8 2.7 - - - -
2304 HIS* 4.8 0.9 - - + -
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Residues in contact with VAL 200 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1504 ILE* 3.9 14.8 - - + -
1894 LEU* 3.9 13.0 - - + -
1934 ILE* 3.8 26.2 - - + -
1994 LEU* 1.3 82.3 - - - +
2014 SER* 1.4 61.6 + - - +
2024 VAL* 3.8 23.6 - - + -
2184 ILE* 4.5 0.7 - - + -
2224 CYS* 3.7 33.2 - - - -
2274 VAL* 3.8 8.1 - - + -
2284 TYR 3.3 10.2 + - - +
2294 PHE* 4.0 6.1 - - + -
2304 HIS 3.0 23.0 + - - -
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Residues in contact with SER 201 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1354 ILE* 3.3 39.2 - - - +
1504 ILE* 3.5 13.7 + - - +
1514 THR* 3.8 1.8 - - - -
1524 THR* 3.3 20.8 + - - -
1554 GLU* 3.3 23.7 + - - +
1764 LEU* 5.7 0.7 - - - +
1844 ILE* 5.2 0.2 - - - +
1994 LEU* 4.4 1.3 - - - -
2004 VAL* 1.4 72.8 - - - +
2024 VAL* 1.3 71.9 + - - +
2034 MET* 4.6 0.5 - - - -
2304 HIS* 3.4 14.1 + - - -
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Residues in contact with VAL 202 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1524 THR* 3.9 11.4 - - + +
1544 THR* 5.0 1.8 - - - +
1764 LEU* 5.7 0.4 - - + -
1784 VAL* 5.5 0.2 - - + -
1844 ILE* 3.9 25.8 - - + -
1894 LEU* 5.1 1.3 - - + -
2004 VAL* 3.8 18.1 - - + -
2014 SER* 1.3 80.4 - - - +
2034 MET* 1.3 82.2 + - - +
2134 GLN* 3.9 23.3 - - + +
2184 ILE* 3.9 25.8 - - + -
2294 PHE* 4.1 9.6 - - + -
2304 HIS* 2.9 34.3 + - - +
2314 THR* 3.6 3.1 - - - -
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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