Contacts of the helix formed by residues 1181 - 1201 (chain O) 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 LYS1181 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180O ARG* 1.3 114.5 - - - +
1182O SER* 1.3 67.2 + - - +
1183O ASN* 3.3 20.0 - - - +
1184O ILE* 3.1 14.5 + - + +
1185O ARG* 3.0 27.0 + - - +
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Residues in contact with SER1182 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1185C ARG* 4.8 10.9 + - - -
1181O LYS* 1.3 71.3 - - - +
1183O ASN* 1.3 59.9 + - - +
1185O ARG* 3.1 29.3 + - - +
1186O LYS* 2.9 30.7 + - - +
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Residues in contact with ASN1183 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181O LYS* 3.3 23.6 - - - +
1182O SER* 1.3 75.8 + - - +
1184O ILE* 1.3 77.3 + - - +
1186O LYS* 3.5 9.8 + - - +
1187O SER* 3.2 22.7 + - - -
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Residues in contact with ILE1184 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097O PRO* 3.4 39.0 - - + -
1179O GLY* 4.2 2.2 - - - -
1180O ARG* 3.9 47.6 - - + +
1181O LYS* 3.1 15.8 + - + +
1183O ASN* 1.3 91.6 - - - +
1185O ARG* 1.3 62.8 + - - +
1187O SER* 3.4 6.8 + - - -
1188O VAL* 3.1 23.3 + - + +
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Residues in contact with ARG1185 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182I SER* 5.3 6.9 + - - -
1186I LYS* 3.9 18.4 - - - +
1176O MET 4.0 14.5 - - - +
1177O LEU* 3.9 22.7 - - - +
1179O GLY* 3.1 44.0 + - - +
1180O ARG 3.2 21.0 + - - -
1181O LYS 3.0 9.7 + - - +
1182O SER* 3.5 30.6 - - - +
1184O ILE* 1.3 74.5 - - - +
1186O LYS* 1.3 61.0 + - - +
1188O VAL* 3.1 8.8 + - - +
1189O GLN* 2.9 43.3 + - - +
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Residues in contact with LYS1186 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177C LEU* 3.0 42.6 + - + +
1178C GLU 3.6 7.5 + - - -
1179C GLY 2.9 25.1 + - - -
1180C ARG* 4.4 4.8 + - - +
1185C ARG* 3.8 27.5 - - - +
1182O SER* 2.9 17.2 + - - +
1183O ASN* 3.8 8.5 - - - +
1184O ILE 3.2 0.2 - - - -
1185O ARG* 1.3 77.8 - - - +
1187O SER* 1.3 56.8 + - - +
1189O GLN* 3.2 12.1 + - - +
1190O ILE* 2.9 39.5 + - + +
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Residues in contact with SER1187 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099O TYR* 3.1 28.6 + - - -
1183O ASN 3.2 11.6 + - - -
1184O ILE* 3.7 9.6 - - - -
1185O ARG 3.3 0.2 - - - -
1186O LYS* 1.3 79.2 - - - +
1188O VAL* 1.3 62.5 + - - +
1190O ILE* 3.4 11.4 + - - +
1191O ALA 3.0 17.2 + - - -
1194O ARG* 5.6 0.2 + - - -
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Residues in contact with VAL1188 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090O TRP* 3.8 26.9 - - + -
1097O PRO* 4.4 17.3 - - + -
1098O SER 3.8 12.3 - - - +
1099O TYR* 3.6 29.4 - - + -
1100O PRO* 3.8 2.2 - - + +
1175O LYS 4.7 1.6 - - - +
1176O MET* 3.9 23.6 - - + +
1179O GLY 6.0 0.4 - - - +
1184O ILE* 3.1 18.3 + - + +
1185O ARG* 3.5 10.8 - - - +
1186O LYS 3.1 0.2 - - - -
1187O SER* 1.3 77.8 - - - +
1189O GLN* 1.3 55.6 + - - +
1191O ALA* 3.2 5.6 + - - +
1192O TYR* 2.9 24.8 + - - +
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Residues in contact with GLN1189 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177C LEU* 3.7 27.3 - - + +
1176O MET* 3.9 29.3 + - + +
1185O ARG* 2.9 34.0 + - - +
1186O LYS* 3.2 12.2 + - - +
1188O VAL* 1.3 73.0 - - - +
1190O ILE* 1.3 67.0 + - - +
1192O TYR* 3.1 8.1 + - - +
1193O HIS* 3.0 36.1 + - + +
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Residues in contact with ILE1190 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174C GLU* 4.1 18.9 - - + +
1177C LEU* 3.6 43.1 - - + +
1178C GLU* 5.0 3.4 - - - -
1186O LYS* 2.9 32.0 + - - +
1187O SER* 3.7 8.3 - - - +
1189O GLN* 1.3 76.4 - - - +
1191O ALA* 1.3 63.8 + - - +
1193O HIS* 3.2 6.7 + - - +
1194O ARG* 2.9 59.5 + - - +
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Residues in contact with ALA1191 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099O TYR* 3.4 39.7 - - + +
1100O PRO* 3.7 11.1 - - + +
1148O PHE* 3.5 27.7 - - + +
1187O SER 3.0 6.0 + - - +
1188O VAL 3.2 8.9 + - - +
1190O ILE* 1.3 76.0 - - - +
1192O TYR* 1.3 56.7 + - - +
1194O ARG* 3.3 6.1 + - - +
1195O ALA* 2.8 26.2 + - - +
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Residues in contact with TYR1192 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090O TRP* 3.6 20.0 - + - -
1100O PRO* 3.6 10.3 - - + -
1165O LEU* 3.9 20.0 - - + -
1166O GLY* 4.5 1.0 - - - -
1169O GLN* 5.4 3.6 - - - +
1172O ASP* 2.8 47.6 + - + +
1176O MET* 3.8 29.8 - - + -
1188O VAL 2.9 13.3 + - - +
1189O GLN 3.4 7.9 - - - +
1191O ALA* 1.3 78.0 - - - +
1193O HIS* 1.3 83.0 + + - +
1195O ALA* 3.1 5.5 + - - +
1196O LEU* 3.0 48.2 + - + +
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Residues in contact with HIS1193 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1170C ASP* 3.3 42.1 - - - +
1173C LYS* 3.5 41.8 + - + +
1174C GLU* 4.1 10.4 + - + +
1177C LEU* 4.3 12.3 - - + +
1176O MET* 5.4 3.1 - - - -
1189O GLN* 3.0 29.5 + - + -
1190O ILE 3.8 5.6 - - - +
1192O TYR* 1.3 97.0 - + - +
1194O ARG* 1.3 56.0 + - - +
1196O LEU* 3.2 2.0 + - - +
1197O GLN* 2.9 34.9 + - - +
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Residues in contact with ARG1194 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174C GLU* 3.1 31.1 + - - +
1099O TYR* 4.8 2.8 + - - -
1148O PHE* 2.9 41.4 + - + -
1149O ASP* 3.4 2.8 + - - +
1150O ASN* 2.6 43.8 + - - +
1152O ARG* 6.5 0.2 - - - +
1190O ILE* 2.9 38.9 + - - +
1191O ALA* 3.4 8.1 - - - +
1193O HIS* 1.3 72.8 - - - +
1195O ALA* 1.4 64.8 + - - +
1197O GLN* 3.2 10.9 + - - +
1198O HIS* 3.0 21.8 + - - +
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Residues in contact with ALA1195 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088O LEU* 3.5 13.7 - - + +
1100O PRO* 4.2 6.3 - - + -
1148O PHE* 3.7 32.0 - - + -
1165O LEU* 4.0 22.0 - - + -
1191O ALA 2.8 16.3 + - - +
1192O TYR 3.1 9.4 + - - +
1194O ARG* 1.4 72.0 - - - +
1196O LEU* 1.3 64.8 + - - +
1198O HIS* 3.2 4.9 + - - +
1199O ARG 3.1 16.8 + - - -
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Residues in contact with LEU1196 (chain O).
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* 3.6 36.1 - - - +
1088O LEU* 4.3 2.7 - - + -
1165O LEU* 3.7 27.4 - - + -
1166O GLY* 4.5 4.0 - - - -
1192O TYR* 3.0 42.1 + - + +
1193O HIS 3.2 2.7 + - - +
1195O ALA* 1.3 80.1 - - - +
1197O GLN* 1.3 58.9 + - - +
1199O ARG* 3.4 41.2 + - - +
1200O SER* 3.0 28.6 + - - -
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Residues in contact with GLN1197 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1168C ASN* 4.0 9.5 - - - +
1170C ASP* 3.6 12.8 - - + +
1171C LEU* 3.4 47.3 - - - +
1174C GLU* 2.7 29.1 + - - +
1193O HIS 2.9 24.2 + - - +
1194O ARG* 3.2 8.7 + - - +
1196O LEU* 1.3 75.3 - - - +
1198O HIS* 1.3 59.7 + - - +
1200O SER* 3.4 7.0 + - - -
1201O LYS* 2.9 43.1 + - + +
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Residues in contact with HIS1198 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086O LEU 5.1 2.5 + - - -
1088O LEU* 4.4 9.2 - - + -
1102O LEU* 3.9 32.4 - - + +
1115O HIS* 4.8 6.4 - + - -
1118O VAL* 3.7 30.1 - - + +
1120O ILE* 4.1 17.4 - - + +
1148O PHE* 3.8 19.5 - + + -
1152O ARG* 5.7 2.0 + - - -
1194O ARG 3.0 12.8 + - - +
1195O ALA 3.2 8.0 + - - +
1197O GLN* 1.3 76.4 - - - +
1199O ARG* 1.3 66.3 + - - +
1201O LYS* 3.5 9.0 + - - +
1202O VAL* 3.1 35.4 + - + +
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Residues in contact with ARG1199 (chain O).
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* 5.7 0.4 + - - -
1088O LEU* 4.0 17.5 - - + -
1165O LEU 4.8 1.6 + - - -
1166O GLY* 2.8 35.6 + - - -
1195O ALA 3.1 12.1 + - - +
1196O LEU* 3.4 38.3 + - - +
1198O HIS* 1.3 79.3 - - - +
1200O SER* 1.3 58.2 + - - +
1202O VAL* 2.6 39.4 + - + +
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Residues in contact with SER1200 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1168C ASN* 3.6 24.1 + - - -
1170C ASP* 5.6 3.4 - - - -
1196O LEU 3.0 14.2 + - - -
1197O GLN* 3.4 8.2 + - - -
1199O ARG* 1.3 79.1 - - - +
1201O LYS* 1.3 65.6 + - - +
1202O VAL 3.1 8.0 + - - +
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Residues in contact with LYS1201 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1168C ASN* 6.0 1.8 - - - +
1116O HIS 4.2 6.2 - - - +
1118O VAL* 3.9 26.4 - - + +
1197O GLN* 2.9 33.2 + - + +
1198O HIS* 3.7 9.4 - - - +
1199O ARG 3.1 0.2 - - - -
1200O SER* 1.3 77.4 + - - +
1202O VAL* 1.3 60.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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