Contacts of the helix formed by residues 2175 - 2181 (chain D) in PDB entry 2C5L
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 SER2175 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLN* 3.7 16.6 + - - +
2145D SER* 2.7 38.5 + - - -
2147D GLU* 3.7 8.8 + - - +
2148D GLN* 4.2 5.0 + - - +
2172D ALA* 3.0 21.5 + - - +
2174D TYR* 1.3 75.8 - - - +
2176D LEU* 1.3 55.5 + - - +
2177D SER* 3.3 1.3 - - - -
2178D ILE* 3.2 5.9 + - - +
2179D LEU* 2.7 34.4 + - - +
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Residues in contact with LEU2176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2147D GLU* 4.1 12.3 + - - +
2174D TYR 3.4 5.6 + - - +
2175D SER* 1.3 72.5 - - - +
2177D SER* 1.3 56.9 + - - +
2179D LEU* 3.4 26.1 - - + +
2180D SER* 3.0 29.0 + - - -
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Residues in contact with SER2177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2144D VAL 4.7 0.5 + - - -
2145D SER* 3.5 26.3 - - - -
2146D PRO* 3.7 15.0 - - - +
2147D GLU* 5.1 0.6 + - - -
2175D SER* 4.4 0.2 - - - -
2176D LEU* 1.3 79.2 - - - +
2178D ILE* 1.3 69.7 + - - +
2180D SER* 3.4 18.0 - - - -
2181D ASN* 3.5 11.6 + - - +
2187D TYR* 4.4 1.6 + - - -
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Residues in contact with ILE2178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2144D VAL* 3.3 31.9 - - + +
2145D SER* 4.7 1.3 - - - -
2169D LEU* 3.7 41.1 - - + +
2172D ALA* 3.5 44.4 - - + +
2173D LYS* 4.6 2.7 - - - +
2175D SER* 3.2 3.9 + - - +
2177D SER* 1.3 80.1 + - - +
2179D LEU* 1.3 65.1 + - - +
2180D SER 3.1 2.0 - - - -
2181D ASN 3.0 21.7 + - - +
2182D PRO* 3.5 5.0 - - + +
2187D TYR* 4.1 15.0 - - + +
2233D LEU* 4.0 9.6 - - + -
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Residues in contact with LEU2179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2173D LYS* 3.9 20.6 + - - +
2174D TYR* 4.2 17.9 - - + +
2175D SER 2.7 18.6 + - - +
2176D LEU* 3.4 28.0 - - + +
2178D ILE* 1.3 73.5 - - - +
2180D SER* 1.3 61.7 + - - +
2182D PRO* 3.9 12.3 - - - +
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Residues in contact with SER2180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2176D LEU* 3.0 16.9 + - - -
2177D SER* 3.4 13.9 - - - -
2179D LEU* 1.3 79.8 - - - +
2181D ASN* 1.3 70.0 + - - +
2182D PRO* 3.4 8.0 - - - +
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Residues in contact with ASN2181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2169D LEU* 4.4 2.6 - - - +
2177D SER 3.5 6.1 + - - +
2178D ILE 3.0 9.3 + - - +
2180D SER* 1.3 98.1 + - - +
2182D PRO* 1.4 59.2 - - - +
2183D ASN* 3.0 11.8 + - - +
2186D ASP* 5.0 11.4 - - - +
2187D TYR* 3.1 38.3 + - + +
2235D LEU* 3.8 23.0 - - + +
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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