Contacts of the helix formed by residues 2308 - 2318 (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 THR2308 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2307C LEU* 1.3 76.5 - - - +
2309C ASP* 1.3 59.6 + - - +
2310C GLU* 3.1 20.6 + - - +
2311C GLY 3.0 19.2 + - - -
2312C TYR* 2.9 27.7 + - - -
2332C THR 3.7 15.2 + - - +
2333C PHE* 2.9 27.9 + - - +
2335C THR* 4.0 22.0 - - + -
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Residues in contact with ASP2309 (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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2286C ARG* 3.5 35.5 + - - +
2307C LEU 4.0 0.7 + - - +
2308C THR* 1.3 73.3 - - - +
2310C GLU* 1.3 69.4 + - - +
2312C TYR* 3.2 7.3 + - - +
2313C GLN* 3.1 22.1 + - - +
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Residues in contact with GLU2310 (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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2308C THR* 3.1 22.3 + - - +
2309C ASP* 1.3 77.9 + - - +
2311C GLY* 1.3 61.3 + - - +
2313C GLN* 3.2 15.8 + - - +
2314C TRP* 3.0 23.7 + - - +
2333C PHE* 4.1 18.4 - - + -
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Residues in contact with GLY2311 (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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2274C VAL* 3.5 9.7 - - - +
2307C LEU* 3.8 15.7 - - - -
2308C THR* 3.0 17.1 + - - -
2310C GLU* 1.3 74.3 - - - +
2312C TYR* 1.3 63.5 + - - +
2314C TRP* 3.4 0.9 + - - -
2315C GLY* 3.0 20.4 + - - -
2333C PHE* 3.7 27.1 - - - -
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Residues in contact with TYR2312 (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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2277C HIS* 3.1 40.1 + + - -
2278C SER* 2.9 26.6 + - - -
2281C PHE* 3.9 4.3 - - - +
2282C ALA* 3.7 40.4 - - + +
2285C LYS 4.1 0.3 + - - -
2286C ARG* 2.6 73.6 + - + +
2288C CYS 4.1 0.3 + - - -
2307C LEU* 3.3 31.1 - - + +
2308C THR 2.9 26.4 + - - -
2309C ASP* 3.2 3.8 + - - +
2311C GLY* 1.3 75.2 - - - +
2313C GLN* 1.3 60.7 + - - +
2316C GLU* 3.3 10.6 + - - +
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Residues in contact with GLN2313 (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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2286C ARG* 5.7 1.1 - - - +
2309C ASP 3.1 11.3 + - - +
2310C GLU* 3.4 18.6 - - - +
2311C GLY 3.1 0.2 - - - -
2312C TYR* 1.3 75.3 - - - +
2314C TRP* 1.3 65.3 + - - +
2316C GLU* 3.2 6.7 + - - +
2317C GLU* 3.1 44.3 + - + +
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Residues in contact with TRP2314 (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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2271C ALA* 3.9 37.9 - - + -
2274C VAL* 3.7 16.4 - - + -
2275C ALA* 4.9 1.1 - - + -
2310C GLU 3.0 8.9 + - - +
2311C GLY 4.0 1.1 - - - +
2313C GLN* 1.3 75.4 - - - +
2315C GLY* 1.3 64.6 + - - +
2317C GLU* 3.1 16.6 + - - +
2318C ASN* 2.8 64.9 + - + +
2323C ASN* 4.1 15.0 - - - -
2326C SER* 4.0 12.3 - - - -
2327C GLU* 2.8 27.6 + - - -
2328C GLY* 3.2 20.3 + - - -
2329C PHE* 3.8 21.1 - + + -
2333C PHE* 3.5 28.5 - + + -
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Residues in contact with GLY2315 (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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2274C VAL* 3.9 9.2 - - - -
2275C ALA* 3.9 12.3 - - - +
2278C SER* 3.6 18.6 - - - -
2279C LYS 5.4 0.2 + - - -
2311C GLY 3.0 16.4 + - - -
2313C GLN 3.2 0.2 - - - -
2314C TRP* 1.3 91.0 - - - +
2316C GLU* 1.3 56.9 + - - +
2318C ASN 3.6 3.4 - - - +
2319C LYS* 3.5 19.6 + - - +
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Residues in contact with GLU2316 (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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2278C SER* 3.8 8.3 - - - +
2279C LYS* 6.5 0.9 - - - -
2282C ALA* 5.9 4.0 - - + -
2312C TYR 3.3 14.3 + - - +
2313C GLN* 3.2 6.5 + - - +
2314C TRP 3.1 0.8 - - - -
2315C GLY* 1.3 75.6 - - - +
2317C GLU* 1.3 68.2 + - - +
2319C LYS* 3.4 25.9 - - + +
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Residues in contact with GLU2317 (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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2313C GLN* 3.1 40.8 + - + +
2314C TRP* 3.4 26.9 - - - +
2316C GLU* 1.3 79.7 - - - +
2318C ASN* 1.3 64.0 + - - +
2319C LYS* 3.2 9.0 + - - +
2320C ASP* 4.6 6.1 - - - +
2327C GLU* 5.6 1.6 - - - +
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Residues in contact with ASN2318 (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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2275C ALA* 3.9 12.8 - - - +
2314C TRP* 2.8 66.1 + - + +
2315C GLY* 3.6 7.6 - - - +
2317C GLU* 1.3 76.8 - - - +
2319C LYS* 1.3 58.9 + - - +
2320C ASP* 3.0 20.9 + - + +
2323C ASN* 4.1 10.4 + - - +
2325C LEU* 5.2 9.5 - - - +
2326C SER 5.3 1.2 - - - +
2327C GLU* 3.0 31.8 + - - +
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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