Contacts of the strand formed by residues 2224 - 2231 (chain A) in PDB entry 4YNP
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 CYS2224 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2166A ILE* 3.5 28.3 - - - -
2222A PRO* 3.5 6.2 - - - +
2223A ASN* 1.3 98.6 - - - +
2225A GLU* 1.3 62.0 + - - +
2239A LEU* 3.7 22.4 - - + -
2240A TYR 3.3 7.0 - - - +
2241A ALA* 4.5 0.7 - - - -
2242A LEU* 3.4 11.6 - - - +
2245A MET* 4.2 3.8 - - - -
2251A LEU* 3.7 20.2 - - - -
2252A THR 2.9 19.7 + - - +
2253A TYR* 3.4 10.0 - - - +
2254A ASP 4.6 0.5 + - - -
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Residues in contact with GLU2225 (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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2224A CYS* 1.3 78.9 - - - +
2226A MET* 1.3 69.9 + - - +
2227A GLN* 3.3 29.5 + - - +
2238A GLY 3.6 0.7 - - - +
2239A LEU* 3.5 6.3 - - - +
2240A TYR* 2.8 39.5 + - - +
2242A LEU* 3.5 29.5 - - + +
2253A TYR* 4.5 2.5 - - - -
2258A HIS* 5.0 7.4 - - + +
2071B LYS* 4.9 10.1 + - - -
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Residues in contact with MET2226 (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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2169A TYR* 3.7 29.2 - - + -
2196A LEU* 3.8 13.9 - - + -
2213A ALA* 4.9 3.6 - - + +
2216A ILE* 5.0 3.4 - - + -
2225A GLU* 1.3 77.0 - - - +
2227A GLN* 1.3 63.0 + - - +
2228A LYS 4.2 0.5 + - - -
2237A ILE* 3.8 25.4 - - + -
2238A GLY 3.6 0.9 - - - -
2239A LEU* 3.6 28.9 - - + -
2253A TYR* 3.4 49.6 - - + -
2258A HIS* 3.6 33.2 + - + +
2071B LYS* 5.7 3.1 + - - -
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Residues in contact with GLN2227 (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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2114A PHE* 3.3 24.2 - - + -
2163A GLY* 6.2 0.6 - - - -
2225A GLU* 3.3 29.3 + - - +
2226A MET* 1.3 76.3 - - - +
2228A LYS* 1.3 60.8 + - - +
2229A TRP* 3.2 32.4 + - + +
2237A ILE* 3.4 5.6 - - - +
2238A GLY 2.8 35.6 + - - +
2240A TYR* 3.5 33.5 - - + +
2241A ALA 5.7 0.6 + - - -
2073B ARG* 3.3 17.1 + - - +
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Residues in contact with LYS2228 (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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2114A PHE* 3.9 19.8 - - - +
2198A LEU* 3.2 26.4 + - + +
2199A ASP* 2.6 26.4 + - - -
2226A MET 4.2 1.0 + - - -
2227A GLN* 1.3 70.0 - - - +
2229A TRP* 1.3 62.5 + - - +
2230A SER 4.4 0.2 + - - -
2235A TYR* 3.5 42.0 - - + -
2236A ARG 4.0 4.3 - - - +
2237A ILE* 4.6 11.2 - - + +
2069B TYR 5.2 7.5 + - - -
2070B LYS* 6.3 0.2 - - - +
2071B LYS* 6.2 3.6 - - + +
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Residues in contact with TRP2229 (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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2111A ARG* 4.2 17.9 - - + -
2114A PHE* 3.3 38.3 - + - -
2115A ALA 3.7 13.2 - - - -
2116A GLU* 3.8 18.8 - - + -
2130A ASN* 3.4 22.0 - - - -
2132A ARG* 3.4 20.2 - - - -
2133A ILE* 3.8 17.9 - - + -
2227A GLN* 3.2 48.9 + - + +
2228A LYS* 1.3 76.2 - - - +
2230A SER* 1.3 59.9 + - - +
2231A VAL* 3.7 5.3 + - + -
2234A VAL 3.4 0.5 - - - +
2235A TYR* 3.0 11.1 - - - -
2236A ARG 2.8 38.0 + - - +
2240A TYR* 3.1 32.3 + + - -
2073B ARG* 4.2 8.3 - - - -
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Residues in contact with SER2230 (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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2084A SER* 3.0 24.9 + - - -
2086A TYR* 3.4 42.1 + - - -
2114A PHE 3.1 9.8 + - - -
2115A ALA* 3.5 3.8 - - - +
2116A GLU 2.9 26.7 + - - +
2228A LYS 4.4 0.2 + - - -
2229A TRP* 1.3 69.0 - - - +
2231A VAL* 1.3 62.0 + - - +
2232A ASN 4.2 0.9 + - - -
2233A GLY 4.1 7.1 + - - -
2234A VAL 3.5 4.3 - - - -
2235A TYR* 4.1 5.6 - - - -
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Residues in contact with VAL2231 (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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2116A GLU* 3.4 39.7 - - + +
2133A ILE* 3.7 25.6 - - + -
2134A GLN* 3.5 25.4 - - + +
2229A TRP* 4.1 6.7 - - + +
2230A SER* 1.3 74.4 + - - +
2232A ASN* 1.3 63.9 + - + +
2234A VAL* 2.6 42.1 + - - +
2236A ARG* 4.1 26.9 + - + +
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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