Contacts of the helix formed by residues 1220 - 1231 (chain J) in PDB entry 4XLN
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 ALA1220 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1041I GLU 4.2 12.4 + - - +
1042I ALA* 4.6 0.9 - - - +
1044I GLY* 5.9 0.2 - - - -
1105J ILE 3.7 8.5 - - - +
1106J VAL* 3.6 22.9 - - + -
1218J GLY 3.3 3.2 + - - -
1219J GLU* 1.3 74.9 + - - +
1221J VAL* 1.3 62.2 + - - +
1222J GLY 3.3 0.8 + - - -
1223J VAL* 4.3 7.4 - - + +
1224J VAL* 3.2 26.9 + - - +
1462J LEU* 4.0 13.0 - - + -
1474J ALA* 3.7 13.9 - - + +
1475J GLY* 5.0 0.6 - - - +
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Residues in contact with VAL1221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105J ILE* 3.5 11.5 + - + +
1107J VAL* 3.8 22.4 - - + +
1200J VAL* 3.6 26.9 - - + -
1205J TYR* 3.6 36.0 + - + +
1215J VAL* 4.2 1.1 - - + -
1219J GLU* 3.4 15.0 + - + -
1220J ALA* 1.3 74.3 - - - +
1222J GLY* 1.3 62.0 + - - +
1223J VAL 3.4 0.4 - - - -
1224J VAL* 4.0 7.4 - - + +
1225J ALA* 2.9 32.3 + - - +
1370J ILE* 3.6 17.0 - - + +
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Residues in contact with GLY1222 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102J ALA* 3.2 35.9 - - - +
1105J ILE* 3.2 18.5 + - - -
1221J VAL* 1.3 78.7 - - - +
1223J VAL* 1.3 59.6 + - - +
1225J ALA* 3.7 4.3 - - - +
1226J ALA* 2.9 30.3 + - - +
1370J ILE* 4.6 2.7 - - - -
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Residues in contact with VAL1223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038I TRP* 3.2 44.6 - - + +
1041I GLU* 3.7 24.0 - - + +
1042I ALA* 4.2 9.2 - - + +
1099J VAL* 5.1 8.1 - - + -
1103J HIS* 4.0 17.0 - - + +
1220J ALA* 4.0 10.7 + - + +
1222J GLY* 1.3 73.2 - - - +
1224J VAL* 1.3 59.7 + - - +
1226J ALA* 3.3 6.0 + - - +
1227J GLU* 2.9 36.3 + - + +
1462J LEU* 3.9 18.8 - - + -
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Residues in contact with VAL1224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042I ALA* 3.5 36.1 - - + +
710J ARG* 4.2 9.9 - - + +
772J PRO* 4.2 26.5 - - + +
1205J TYR* 5.2 4.0 - - - +
1219J GLU* 4.1 8.3 - - + +
1220J ALA 3.2 20.8 + - - +
1221J VAL* 4.0 7.9 - - + +
1222J GLY 3.4 0.4 - - - -
1223J VAL* 1.3 76.5 - - - +
1225J ALA* 1.3 54.5 + - - +
1227J GLU* 3.4 4.3 + - - +
1228J SER* 2.6 43.8 + - - +
1367J HIS* 4.8 5.2 - - + -
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Residues in contact with ALA1225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102J ALA* 6.0 0.4 - - + -
1221J VAL 2.9 21.4 + - - +
1222J GLY* 3.7 4.0 - - - +
1224J VAL* 1.3 74.9 - - - +
1226J ALA* 1.3 64.9 + - - +
1228J SER* 2.9 2.9 + - - -
1229J ILE* 2.9 30.7 + - + +
1367J HIS* 3.4 49.1 + - + +
1370J ILE* 4.1 8.7 - - + -
1371J VAL* 5.5 2.0 - - + -
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Residues in contact with ALA1226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095J THR* 4.6 4.5 - - - +
1098J LEU* 3.9 23.7 - - + +
1099J VAL* 3.8 41.1 - - + +
1102J ALA* 5.0 1.8 - - + +
1222J GLY 2.9 17.5 + - - +
1223J VAL* 3.6 6.1 - - - +
1225J ALA* 1.3 75.9 - - - +
1227J GLU* 1.3 57.5 + - - +
1229J ILE* 3.5 4.3 + - - +
1230J GLY* 2.9 24.3 + - - -
1371J VAL* 5.8 2.2 - - + +
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Residues in contact with GLU1227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035I MET 3.7 4.5 - - - +
1038I TRP* 3.3 23.6 - - + +
1039I ALA* 3.0 31.0 + - - +
1042I ALA* 3.3 11.7 - - - +
707J THR* 5.2 0.9 - - - +
708J LEU 3.1 26.0 - - - +
709J HIS* 3.9 6.9 + - - +
710J ARG* 3.2 28.2 - - - +
1095J THR* 5.4 3.8 - - + -
1099J VAL* 5.3 1.6 - - + -
1223J VAL* 2.9 21.3 + - + +
1224J VAL* 3.7 4.9 - - - +
1226J ALA* 1.3 74.2 - - + +
1228J SER* 1.3 60.0 + - - +
1230J GLY* 4.2 2.0 - - - +
1231J GLU* 2.9 32.4 + - - +
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Residues in contact with SER1228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709J HIS* 4.0 12.6 - - - -
772J PRO* 4.1 3.5 + - - +
773J ALA* 3.7 29.5 + - - +
1224J VAL* 2.6 23.2 + - - +
1225J ALA 2.9 9.4 + - - -
1227J GLU* 1.3 77.7 - - - +
1229J ILE* 1.3 57.7 + - - +
1231J GLU* 4.4 2.8 - - - +
1232J PRO* 3.1 22.7 - - - +
1363J LEU* 4.9 7.4 - - - +
1367J HIS* 3.9 23.6 - - - -
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Residues in contact with ILE1229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094J LEU* 5.3 3.2 - - + +
1098J LEU* 3.7 32.1 - - + -
1225J ALA 2.9 16.5 + - - +
1226J ALA* 3.9 0.4 - - - +
1228J SER* 1.3 76.9 - - - +
1230J GLY* 1.3 64.9 + - - +
1231J GLU 3.4 0.2 - - - -
1232J PRO* 3.2 10.9 - - - +
1233J GLY* 3.8 3.8 + - - -
1263J PHE* 4.1 20.0 - - + -
1356J TYR* 3.3 34.3 + - + +
1363J LEU* 5.3 7.2 - - + -
1367J HIS* 4.1 10.5 - - + -
1368J ILE* 4.0 22.9 - - + +
1371J VAL* 3.9 23.1 - - + -
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Residues in contact with GLY1230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708J LEU* 4.8 7.8 - - - +
1091J SER* 3.7 9.7 + - - -
1095J THR* 3.4 28.3 + - - -
1098J LEU* 5.6 0.7 - - - -
1226J ALA 2.9 16.9 + - - -
1227J GLU 3.1 4.2 + - - -
1229J ILE* 1.3 76.9 - - - +
1231J GLU* 1.3 64.5 + - - +
1233J GLY* 3.1 14.8 + - - -
1234J THR* 4.4 0.3 + - - +
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Residues in contact with GLU1231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708J LEU* 3.6 31.0 - - + +
709J HIS* 3.3 46.5 + - + +
773J ALA* 5.4 1.4 - - - +
1227J GLU 2.9 7.8 + - - +
1228J SER 4.4 0.7 - - - +
1230J GLY* 1.3 76.9 - - - +
1232J PRO* 1.3 82.7 - - + +
1233J GLY 3.1 0.3 + - - -
1234J THR* 3.1 19.2 + - - -
1235J GLN* 3.6 12.1 + - - +
1361J VAL* 5.3 1.4 - - - +
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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
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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