Contacts of the helix formed by residues 1168 - 1177 (chain C) in PDB entry 2X4Y
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 ASN1168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1164C PRO 5.6 0.2 + - - -
1166C GLY 3.7 0.6 - - - +
1167C VAL* 1.3 88.0 - - + +
1169C GLN* 1.3 56.8 + - - +
1170C ASP* 3.1 13.2 + - - +
1171C LEU* 3.0 36.9 + - + +
1172C ASP* 3.0 31.5 + - - -
1197O GLN* 4.0 9.1 - - - +
1200O SER* 3.6 23.2 + - - -
1201O LYS* 6.0 2.0 - - - +
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Residues in contact with GLN1169 (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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1167C VAL 4.2 0.8 - - - -
1168C ASN* 1.3 72.5 + - - +
1170C ASP* 1.3 64.7 + - - +
1172C ASP* 3.4 9.5 + - - +
1173C LYS* 3.0 58.2 + - - +
1192C TYR* 5.6 0.4 - - - -
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Residues in contact with ASP1170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1168C ASN* 3.1 9.1 + - - +
1169C GLN* 1.3 81.6 - - - +
1171C LEU* 1.3 60.3 + - - +
1173C LYS* 4.8 3.8 + - - +
1174C GLU* 2.9 28.9 + - - +
1193O HIS* 3.3 46.4 - - + +
1196O LEU* 3.6 36.9 - - + +
1197O GLN* 3.6 8.5 - - + +
1199O ARG* 5.7 0.3 + - - -
1200O SER* 5.6 3.6 - - - -
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Residues in contact with LEU1171 (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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1090C TRP* 3.8 12.3 - - + +
1163C VAL* 3.6 34.1 - - + -
1164C PRO 4.2 5.2 - - - +
1168C ASN* 3.0 28.8 + - + +
1170C ASP* 1.3 75.1 - - - +
1172C ASP* 1.3 62.8 + - - +
1174C GLU* 3.3 4.6 + - - +
1175C LYS* 2.8 54.5 + - + +
1197O GLN* 3.4 29.2 - - - +
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Residues in contact with ASP1172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090C TRP* 2.9 25.4 + - - +
1164C PRO 4.4 0.5 - - - +
1165C LEU* 3.9 1.2 - - - -
1166C GLY* 3.0 34.0 + - - -
1167C VAL 4.6 0.2 + - - -
1168C ASN 3.0 17.6 + - - +
1169C GLN* 3.6 11.1 - - - +
1171C LEU* 1.3 79.8 - - - +
1173C LYS* 1.3 57.9 + - + +
1175C LYS* 3.3 2.8 + - - +
1176C MET* 2.9 34.7 + - + +
1192C TYR* 2.8 41.0 + - + +
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Residues in contact with LYS1173 (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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1169C GLN* 3.0 43.9 + - - +
1170C ASP* 3.9 2.6 + - - +
1171C LEU 3.3 0.2 - - - -
1172C ASP* 1.3 73.9 - - + +
1174C GLU* 1.3 69.0 + - - +
1176C MET* 3.3 25.3 + - + +
1177C LEU* 3.3 19.3 + - + +
1193O HIS* 3.5 41.6 + - + +
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Residues in contact with GLU1174 (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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1170C ASP 2.9 17.8 + - - +
1171C LEU* 3.5 6.1 - - - +
1173C LYS* 1.3 76.1 - - - +
1175C LYS* 1.3 69.6 + - + +
1177C LEU* 3.1 21.4 + - - +
1178C GLU* 3.7 5.9 + - - +
1190O ILE* 4.1 18.8 - - + +
1193O HIS* 4.1 13.7 - - + +
1194O ARG* 3.1 36.3 + - + +
1197O GLN* 2.7 33.5 + - - +
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Residues in contact with LYS1175 (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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1090C TRP* 3.6 37.3 - - + +
1092C LYS* 5.9 1.0 - - - +
1097C PRO* 5.5 0.7 - - - +
1098C SER* 3.2 36.4 + - - +
1163C VAL* 4.0 25.4 - - - +
1171C LEU* 2.8 45.9 + - + +
1172C ASP 3.6 0.4 - - - +
1174C GLU* 1.3 81.4 - - + +
1176C MET* 1.3 61.9 + - - +
1177C LEU 3.1 1.2 + - - -
1178C GLU* 3.2 30.0 + - - +
1179C GLY 4.9 0.2 + - - -
1188C VAL* 4.6 3.3 - - - +
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Residues in contact with MET1176 (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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1090C TRP* 3.5 20.9 - - + -
1172C ASP* 2.9 18.8 + - + +
1173C LYS* 3.3 23.0 + - + +
1175C LYS* 1.3 75.3 - - - +
1177C LEU* 1.3 61.5 + - + +
1178C GLU 3.3 1.2 + - - -
1179C GLY 4.7 0.3 + - - -
1185C ARG* 4.0 23.6 - - - +
1188C VAL* 4.1 16.7 - - + +
1189C GLN* 4.1 27.2 + - + +
1192C TYR* 3.6 43.3 - - + -
1193C HIS* 5.0 5.6 - - + +
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Residues in contact with LEU1177 (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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1173C LYS 3.4 15.0 - - - +
1174C GLU 3.1 8.4 + - - +
1175C LYS 3.0 1.4 - - - -
1176C MET* 1.3 81.4 - - + +
1178C GLU* 1.3 57.5 + - - +
1179C GLY 3.5 1.8 - - - -
1185C ARG* 4.1 10.8 - - - +
1189C GLN* 6.0 2.9 - - - +
1186O LYS* 3.0 43.8 + - + +
1189O GLN* 3.7 44.6 - - + +
1190O ILE* 3.6 27.5 - - + +
1193O HIS* 4.3 9.0 - - + +
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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