Contacts of the strand formed by residues 2136 - 2142 (chain C) 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 SER2136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2134C GLU* 4.4 3.6 + - - +
2135C GLU* 1.3 83.4 + - - +
2137C PHE* 1.3 61.3 + - - +
2138C PHE* 5.8 1.9 - - - -
2154C LYS* 3.8 35.8 - - - +
2155C ALA 3.2 14.3 + - - -
2156C PRO* 4.7 2.1 - - - +
2157C ARG* 2.9 24.8 + - - +
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Residues in contact with PHE2137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2136C SER* 1.3 75.6 - - - +
2138C PHE* 1.3 75.7 + - - +
2139C VAL* 3.6 24.0 + - + -
2153C ILE 3.8 0.2 - - - +
2154C LYS* 3.5 2.6 - - - -
2155C ALA* 2.9 49.6 + - + +
2156C PRO 3.5 18.6 - - - -
2157C ARG* 3.8 20.4 - - + +
2159C SER* 4.8 2.7 - - - -
2164C VAL* 5.0 1.1 - - + -
2218C VAL* 3.9 13.5 - - + -
2219C PHE* 3.7 50.3 - + + -
2222C GLN* 3.4 32.1 - - - -
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Residues in contact with PHE2138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 3.9 16.2 - - + -
63A GLU* 4.8 3.6 - - - -
64A TYR* 3.4 41.3 - + - -
1169A GOL 4.0 35.9 + - - +
2136C SER 5.8 1.3 - - - -
2137C PHE* 1.3 88.6 - - - +
2139C VAL* 1.3 60.5 + - - +
2152C VAL* 4.3 4.5 - - + -
2153C ILE 3.3 4.5 - - - +
2154C LYS* 3.8 34.8 - - + -
2222C GLN* 3.7 9.5 + - - +
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Residues in contact with VAL2139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1169A GOL 4.7 0.4 - - - -
2137C PHE* 3.6 29.2 - - + -
2138C PHE* 1.3 74.1 - - - +
2140C GLN* 1.3 67.2 + - - +
2141C VAL* 4.4 9.2 - - + -
2151C THR 3.8 0.5 - - - +
2152C VAL* 3.4 5.1 - - - -
2153C ILE* 3.0 45.1 + - + +
2155C ALA* 4.2 16.8 - - + -
2164C VAL* 4.6 9.2 - - + -
2189C LEU* 6.0 0.2 - - + -
2218C VAL* 4.5 6.1 - - + -
2222C GLN* 4.2 5.8 - - - +
2231C PHE* 3.5 36.8 - - + -
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Residues in contact with GLN2140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLU* 5.0 6.9 - - - +
39A SER* 5.5 0.2 + - - -
1169A GOL 3.8 20.4 + - - +
2139C VAL* 1.3 80.9 - - - +
2141C VAL* 1.3 67.7 + - - +
2142C HIS* 3.5 39.6 + - + +
2150C ARG* 3.8 24.0 + - + +
2151C THR 3.3 12.1 - - - +
2152C VAL* 3.8 23.0 - - + +
2222C GLN* 5.5 0.4 - - - +
2230C LYS* 5.5 0.2 - - - -
2231C PHE* 3.8 12.3 + - - +
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Residues in contact with VAL2141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2139C VAL* 4.4 12.3 - - + +
2140C GLN* 1.3 77.6 - - - +
2142C HIS* 1.3 63.9 + - - +
2144C VAL* 3.5 22.5 - - + +
2150C ARG* 3.3 7.1 - - - +
2151C THR* 2.8 34.6 + - + +
2153C ILE* 4.9 4.5 - - + -
2164C VAL* 4.3 17.5 - - + -
2168C THR* 3.6 26.2 - - + +
2189C LEU* 4.1 15.0 - - + -
2231C PHE* 3.7 5.6 - - + +
2233C LEU* 3.8 26.0 - - + +
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Residues in contact with HIS2142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2140C GLN* 3.5 37.5 + - + +
2141C VAL* 1.3 77.1 - - - +
2143C ASP* 1.3 74.7 + - - +
2144C VAL 3.2 3.6 + - - -
2149C PRO 3.5 4.0 - - - -
2150C ARG* 3.7 22.2 - - - +
2230C LYS* 3.9 43.2 + - + +
2231C PHE 2.9 22.4 + - - +
2232C ILE* 3.6 11.7 - - + -
2233C LEU* 3.0 24.9 + - - +
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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