Contacts of the strand formed by residues 2166 - 2171 (chain B) in PDB entry 6DLP
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 SER2166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2157B ALA* 3.6 4.3 - - - +
2158B THR* 2.9 46.0 + - - +
2159B HIS 5.3 2.4 - - - -
2165B ALA* 1.3 77.0 - - - +
2167B ILE* 1.3 63.0 + - - +
2181B PHE* 3.2 33.9 - - - -
2182B LEU 3.2 14.8 - - - -
2183B ASP* 4.2 4.3 - - - -
2184B LEU* 4.0 8.7 - - - +
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Residues in contact with ILE2167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2155B MET* 3.5 29.6 - - + -
2156B VAL 3.2 24.9 - - - +
2157B ALA* 3.7 7.0 - - + +
2158B THR 4.7 0.2 - - - +
2166B SER* 1.3 74.7 - - - +
2168B TRP* 1.3 63.7 + - - +
2169B LEU* 3.9 18.1 + - + -
2181B PHE* 3.5 7.0 - - - -
2182B LEU* 2.9 59.8 + - + +
2184B LEU* 4.8 8.1 - - + -
2459B MET* 5.9 0.2 - - - -
2471B LEU* 3.7 29.8 - - + -
2493B LEU* 4.3 13.2 - - + -
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Residues in contact with TRP2168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2155B MET* 3.5 5.0 - - - +
2156B VAL* 2.7 50.8 + - + +
2158B THR* 4.0 22.5 - - + +
2167B ILE* 1.3 75.7 - - - +
2169B LEU* 1.3 65.1 + - - +
2179B LEU* 3.6 39.0 - - + -
2180B SER 3.4 13.5 - - - -
2181B PHE* 3.4 40.6 - + + -
2202B LEU* 3.6 7.6 - - + +
2204B LEU* 4.3 17.5 - - + +
2215B ILE* 4.2 26.4 - - + +
2227B ILE* 6.0 2.9 - - + -
2228B ASN 5.8 1.6 - - - -
2229B THR* 4.5 29.6 + - + +
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Residues in contact with LEU2169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2146B LEU* 4.3 15.0 - - + -
2152B VAL* 3.7 34.5 - - + -
2154B CYS 3.6 3.6 - - - +
2155B MET* 3.6 32.5 - - + -
2167B ILE* 3.9 19.7 - - + -
2168B TRP* 1.3 76.0 - - - +
2170B GLY* 1.3 61.3 + - - +
2171B CYS* 5.6 1.1 - - - -
2179B LEU* 3.2 8.3 - - - +
2180B SER* 2.9 42.3 + - - +
2182B LEU* 4.5 6.1 - - + -
2189B TYR* 3.9 28.5 - - + +
2202B LEU* 3.5 5.4 - - - -
2473B LEU* 5.7 0.9 - - + -
2493B LEU* 6.1 1.3 - - + -
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Residues in contact with GLY2170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2152B VAL* 3.5 6.4 - - - -
2153B GLU* 2.9 29.3 + - - -
2154B CYS* 3.2 26.9 + - - -
2169B LEU* 1.3 73.2 - - - +
2171B CYS* 1.3 62.4 + - - -
2178B GLN 3.7 5.4 - - - -
2179B LEU* 4.9 0.4 - - - -
2199B ILE* 4.4 12.1 - - - -
2202B LEU* 3.5 5.6 - - - +
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Residues in contact with CYS2171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2150B VAL* 4.9 1.3 - - - -
2151B ILE 3.4 5.4 - - - -
2152B VAL* 6.4 0.7 - - - -
2153B GLU* 4.5 1.1 - - - -
2169B LEU* 5.6 1.1 - - - -
2170B GLY* 1.3 74.0 - - - -
2172B GLY* 1.3 59.8 + - - +
2173B HIS* 3.4 31.4 - - + +
2174B THR* 4.1 10.0 - - + +
2176B ARG 4.6 2.1 - - - +
2178B GLN* 2.9 42.2 + - + +
2180B SER* 3.0 31.0 - - - -
2189B TYR* 3.6 6.3 - - - -
2198B ARG* 3.7 17.5 - - - +
2199B ILE* 4.4 3.9 + - - +
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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