Contacts of the strand formed by residues 2334 - 2342 (chain C) in PDB entry 4ILG
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 SER2334 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2268C PHE* 3.3 5.7 - - - +
2269C MET* 3.1 49.2 + - - +
2274C VAL* 5.9 0.2 - - - +
2305C TYR* 4.1 9.1 - - - -
2306C ASN 3.3 9.9 - - - -
2331C PRO 3.1 20.8 + - - +
2332C THR* 3.0 7.2 - - - +
2333C PHE* 1.3 79.9 - - - +
2335C THR* 1.3 68.2 + - - +
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Residues in contact with THR2335 (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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2305C TYR* 3.3 11.4 - - - +
2306C ASN* 2.9 49.7 + - - +
2308C THR* 4.0 21.3 - - + -
2332C THR* 4.8 2.7 - - + +
2334C SER* 1.3 79.1 - - - +
2336C HIS* 1.3 63.7 + - - +
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Residues in contact with HIS2336 (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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2172C SER* 3.4 36.2 + - - -
2173C ALA* 3.9 6.7 - - - -
2174C ASP* 4.0 29.0 - - + +
2180C GLN* 2.7 31.2 + - - -
2303C SER* 6.4 0.2 - - - -
2304C ALA 4.0 7.0 - - - -
2305C TYR* 4.8 6.0 - + + -
2306C ASN* 4.7 1.1 - - - +
2335C THR* 1.3 75.8 + - - +
2337C ALA* 1.3 77.1 + - - +
2338C GLN* 4.0 19.3 - - + +
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Residues in contact with ALA2337 (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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2172C SER 4.8 0.9 - - - +
2180C GLN* 3.9 4.7 - - - +
2183C TYR* 4.7 7.2 - - + -
2289C ILE* 4.3 10.8 - - + -
2304C ALA* 3.0 41.8 + - + +
2305C TYR 4.0 6.7 - - - +
2306C ASN* 3.8 17.9 - - - +
2335C THR 3.5 1.0 + - - -
2336C HIS* 1.3 90.8 + - - +
2338C GLN* 1.3 64.6 + - - +
2339C LEU* 3.7 2.4 + - - +
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Residues in contact with GLN2338 (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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2174C ASP 5.3 0.7 - - - +
2175C ASP 4.1 3.5 - - - +
2176C PHE* 3.5 16.0 - - + -
2177C VAL* 2.8 48.2 + - - +
2180C GLN* 3.5 24.4 + - - +
2181C ASN 3.3 24.2 + - - +
2182C VAL* 3.6 18.6 - - + +
2183C TYR* 3.0 32.7 + - - +
2336C HIS* 4.0 18.5 - - + +
2337C ALA* 1.3 75.5 - - - +
2339C LEU* 1.3 60.2 + - - +
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Residues in contact with LEU2339 (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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352A TYR* 3.7 1.9 - - - -
2171C VAL* 3.6 29.3 - - + +
2172C SER 5.1 6.0 + - - +
2173C ALA* 5.8 1.0 - - - +
2183C TYR* 3.4 24.5 - - + +
2185C LEU* 4.3 12.6 - - + -
2221C ILE* 5.2 0.2 - - + -
2291C ILE* 4.1 36.6 - - + -
2302C LEU* 4.0 32.3 - - + -
2303C SER* 4.9 0.2 - - - -
2304C ALA* 4.0 23.6 - - + +
2337C ALA 3.7 1.5 + - - +
2338C GLN* 1.3 77.0 - - - +
2340C LEU* 1.3 81.3 + - - +
2341C LEU* 6.4 0.9 - - + -
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Residues in contact with LEU2340 (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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352A TYR* 3.8 22.9 - - + +
2182C VAL* 3.8 24.7 - - + -
2183C TYR 2.7 13.0 + - - +
2184C VAL* 3.3 14.9 - - + -
2185C LEU* 2.7 34.5 + - - +
2339C LEU* 1.3 87.9 - - - +
2341C LEU* 1.3 58.4 + - - +
2342C SER* 5.8 0.4 - - - -
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Residues in contact with LEU2341 (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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350A LEU* 4.1 23.3 - - + +
352A TYR* 3.0 23.5 + - + +
1863B HIS* 5.7 0.7 + - - -
2169C ILE* 3.9 30.1 - - + -
2171C VAL* 4.8 6.4 - - + +
2185C LEU* 3.5 37.7 - - + +
2187C LYS* 4.0 27.6 - - + -
2190C LEU* 3.9 22.0 - - + -
2302C LEU* 5.0 5.4 - - + -
2339C LEU* 5.1 1.7 - - + +
2340C LEU* 1.3 77.0 - - - +
2342C SER* 1.3 61.7 + - - +
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Residues in contact with SER2342 (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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2184C VAL* 3.6 25.7 - - - +
2185C LEU 3.0 8.5 + - - -
2186C PRO* 3.4 7.3 - - - +
2187C LYS* 2.8 27.4 + - - -
2340C LEU* 5.8 0.2 - - - -
2341C LEU* 1.3 77.7 - - - +
2343C ASP* 1.3 58.3 + - - +
2344C ARG* 3.1 23.4 + - - +
2345C ILE* 3.6 16.1 + - - +
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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