Contacts of the strand formed by residues 2195 - 2199 (chain A) in PDB entry 4YNM
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 CYS2195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2169A TYR* 3.5 6.6 + - - -
2179A PHE* 3.4 34.1 - - + -
2193A HIS* 4.0 2.1 - - + -
2194A TYR* 1.3 79.2 - - - +
2196A LEU* 1.3 62.2 + - - +
2203A VAL* 2.6 41.1 - - - -
2204A ILE 3.2 7.0 - - - -
2205A ASP* 4.4 0.2 - - - -
2207A TYR* 4.4 2.0 - - + +
2253A TYR* 5.5 0.3 + - - -
2259A SER* 3.5 13.8 + - - +
2260A PHE* 3.4 31.5 + - + +
2262A VAL* 5.5 2.7 - - + -
2304A SAM 5.6 0.4 - - - +
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Residues in contact with LEU2196 (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* 3.4 47.5 + - + -
2195A CYS* 1.3 80.2 - - - +
2197A ASN* 1.3 65.5 + - - +
2203A VAL* 3.4 4.2 - - - +
2204A ILE* 2.7 42.1 + - + +
2226A MET* 3.9 8.3 - - + -
2237A ILE* 3.7 30.5 - - + -
2253A TYR* 3.8 33.4 - - + +
2258A HIS* 3.7 23.1 - - + +
2259A SER* 4.2 1.3 - - - +
2260A PHE* 4.4 1.8 - - - -
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Residues in contact with ASN2197 (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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2176A GLU* 5.1 2.8 - - - +
2196A LEU* 1.3 72.9 - - - +
2198A LEU* 1.3 64.5 + - - +
2199A ASP* 5.5 0.8 + - - -
2202A MET 4.2 5.3 - - - +
2203A VAL* 4.6 2.8 - - - +
2237A ILE* 3.3 17.8 - - - +
2257A PHE 4.2 10.5 + - - +
2258A HIS* 2.9 23.2 + - - +
2259A SER 4.1 10.1 + - - -
2260A PHE* 3.5 29.2 - - - +
2261A ASN 5.4 0.6 - - - +
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Residues in contact with LEU2198 (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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2075A ASN* 5.7 0.7 - - - +
2082A PRO* 3.6 36.3 - - + -
2173A VAL* 4.0 19.5 - - + -
2196A LEU 3.5 0.8 + - - -
2197A ASN* 1.3 80.3 - - - +
2199A ASP* 1.3 73.7 + - + +
2202A MET* 2.8 23.2 + - + +
2203A VAL 4.1 2.0 - - - +
2204A ILE* 4.2 22.4 - - + -
2228A LYS* 3.7 14.8 + - + +
2235A TYR* 4.1 25.6 - - + +
2236A ARG* 4.6 0.4 - - - +
2237A ILE* 3.8 26.8 - - + +
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Residues in contact with ASP2199 (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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2197A ASN* 5.2 1.5 + - - +
2198A LEU* 1.3 86.4 - - + +
2200A SER* 1.3 86.5 + - - +
2201A GLY 3.1 2.9 - - - -
2202A MET* 2.7 29.8 + - + +
2228A LYS* 2.2 35.7 + - + +
2235A TYR* 3.6 20.3 - - + -
2068B SER* 5.1 6.8 + - - -
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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