Contacts of the strand formed by residues 2170 - 2175 (chain A) in PDB entry 5ZCS
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 ARG2170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2019A VAL* 4.6 9.0 + - + +
2020A ALA 3.0 27.5 + - - -
2021A ILE* 5.4 1.4 - - - +
2022A LEU* 4.4 9.9 - - - +
2025A GLU* 2.6 38.0 + - - -
2121A LEU* 5.7 5.1 - - - +
2160A LEU* 5.6 3.6 - - + -
2162A VAL* 3.8 20.9 - - + +
2163A ILE* 4.7 2.0 - - - +
2168A ARG* 3.4 37.0 + - - +
2169A PRO* 1.3 82.1 + - - +
2171A LYS* 1.3 61.8 + - - +
2172A LEU* 3.8 3.8 - - + +
2184A PHE 3.8 0.2 - - - +
2185A LEU* 3.3 11.4 - - - +
2186A LEU* 2.9 59.2 + - + -
2187A LYS 6.1 1.4 - - - -
2188A GLY* 6.1 1.8 - - - +
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Residues in contact with LYS2171 (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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2160A LEU* 3.4 11.3 - - - +
2161A GLN* 2.9 50.0 + - + +
2162A VAL* 4.4 1.2 - - - +
2163A ILE* 3.7 28.2 - - + +
2170A ARG* 1.3 72.2 - - - +
2172A LEU* 1.3 60.0 + - - +
2173A THR* 5.5 0.2 - - - -
2183A VAL* 3.7 32.1 - - + -
2184A PHE 3.6 4.3 - - - +
2185A LEU* 4.9 3.6 - - + +
2239A TRP* 4.4 20.8 - - + +
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Residues in contact with LEU2172 (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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2016A LEU* 6.4 2.5 - - + -
2019A VAL* 6.5 1.3 - - + -
2156A ILE* 5.1 7.2 - - + -
2160A LEU* 4.0 20.0 - - + -
2170A ARG* 5.4 2.0 - - + -
2171A LYS* 1.3 76.5 - - - +
2173A THR* 1.3 67.6 + - - +
2174A LEU* 5.1 11.9 - - + -
2183A VAL* 3.4 5.9 - - - +
2184A PHE* 2.9 70.9 + - + +
2186A LEU* 3.8 36.8 - - + -
2236A LEU* 3.9 12.6 - - + -
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Residues in contact with THR2173 (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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2156A ILE* 3.4 23.9 - - - +
2157A ALA* 3.9 26.7 + - + -
2159A SER 5.1 0.9 - - - +
2160A LEU* 4.2 16.9 - - + +
2171A LYS 5.5 0.2 - - - -
2172A LEU* 1.3 77.6 - - - +
2174A LEU* 1.3 68.2 + - - +
2181A GLU* 2.8 30.2 + - - +
2182A PHE 3.2 15.7 + - - -
2183A VAL* 4.5 7.9 - - - +
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Residues in contact with LEU2174 (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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2138A LEU* 6.4 0.2 - - + -
2140A VAL* 5.6 2.2 - - + -
2141A PRO* 4.6 10.3 - - + -
2153A ILE* 3.8 37.2 - - + -
2155A SER 4.9 2.7 - - - +
2156A ILE* 3.8 18.8 - - + +
2157A ALA* 5.8 2.2 - - - +
2172A LEU* 5.1 9.6 - - + -
2173A THR* 1.3 85.0 + - - +
2175A MET* 1.3 63.3 + - - +
2176A GLY 4.1 0.4 - - - -
2181A GLU* 2.9 23.0 - - - +
2182A PHE* 2.9 26.8 + - + +
2184A PHE* 3.7 30.5 - - + -
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Residues in contact with MET2175 (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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2153A ILE* 3.4 10.4 - - - +
2154A GLN* 3.3 41.9 + - + +
2155A SER* 3.8 24.5 + - - +
2156A ILE* 5.8 1.3 - - - -
2157A ALA* 6.0 7.9 - - + +
2174A LEU* 1.3 75.4 - - - +
2176A GLY* 1.3 71.6 + - - +
2179A GLY* 5.7 4.9 - - - -
2180A HIS 5.1 6.1 - - - +
2181A GLU* 3.5 26.2 - - - +
2182A PHE* 5.0 0.4 - - - -
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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