Contacts of the helix formed by residues 1201 - 1206 (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 CYS1201 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1107J VAL* 4.0 7.0 - - - -
1109J GLU 3.3 16.8 - - - +
1110J ALA 3.9 1.1 - - - +
1111J ASP* 4.1 5.6 - - - -
1112J CYS* 3.5 17.7 - - - +
1194J CYS* 3.5 2.6 - - - -
1196J THR* 3.2 16.7 + - - +
1200J VAL* 1.3 74.3 - - - +
1202J GLN* 1.3 65.6 + - - +
1203J LYS* 3.6 5.6 - - - -
1204J CYS* 3.2 17.9 - - - -
1205J TYR* 2.9 24.3 + - - +
2001J ZN 2.3 31.9 - - - -
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Residues in contact with GLN1202 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1107J VAL* 3.9 3.9 - - + +
1109J GLU 3.8 1.4 + - - -
1110J ALA* 3.2 27.3 + - - +
1165J TYR* 3.7 15.8 + - - +
1201J CYS* 1.3 72.6 - - - +
1203J LYS* 1.3 58.7 + - + +
1205J TYR 2.8 5.2 + - - -
1206J GLY* 2.6 32.9 + - - -
1214J PRO* 5.0 6.5 + - - +
1215J VAL* 3.0 40.8 + - + +
1216J SER* 4.6 1.2 - - - +
1217J ILE* 3.4 32.8 - - + +
14K ASP* 5.5 9.9 + - - +
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Residues in contact with LYS1203 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1110J ALA 3.7 7.1 + - - +
1111J ASP* 3.5 27.1 + - + +
1148J VAL* 3.2 38.3 - - + +
1162J GLU* 5.5 5.7 + - - +
1163J GLY* 5.1 14.0 - - - +
1165J TYR* 3.9 18.8 - - + +
1189J ARG* 3.3 48.3 - - - +
1201J CYS* 3.5 2.8 - - - -
1202J GLN* 1.3 78.7 - - + +
1204J CYS* 1.3 58.7 + - - +
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Residues in contact with CYS1204 (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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1112J CYS* 3.6 4.9 - - - -
1114J THR* 4.5 0.7 - - - -
1147J ARG* 3.6 8.0 + - - -
1148J VAL* 5.5 0.3 - - - +
1189J ARG* 2.8 42.7 - - - +
1190J SER 3.7 11.7 - - - +
1191J PRO* 3.6 6.4 - - + +
1193J THR* 4.3 3.4 - - - -
1194J CYS* 3.3 28.9 - - + -
1200J VAL* 5.3 0.7 - - + -
1201J CYS* 3.2 9.5 - - - +
1202J GLN 2.9 1.0 + - - -
1203J LYS* 1.3 77.1 - - - +
1205J TYR* 1.3 63.6 - - - +
2001J ZN 2.2 36.1 - - - -
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Residues in contact with TYR1205 (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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772J PRO 5.3 0.2 + - - -
1146J GLY 3.7 4.2 - - - +
1147J ARG* 4.3 4.3 + - - -
1148J VAL* 5.0 0.9 - - - -
1191J PRO* 4.6 8.7 - - + -
1200J VAL* 4.2 12.1 - - + +
1201J CYS 2.9 15.7 + - - +
1202J GLN 2.8 2.6 + - - +
1203J LYS 4.9 0.2 - - - -
1204J CYS* 1.3 80.0 - - - +
1206J GLY* 1.3 75.2 + - - +
1207J TYR 3.4 8.3 - - - -
1208J ASP* 4.8 2.9 - - - -
1209J LEU* 4.9 3.7 + - + +
1215J VAL* 3.8 20.0 - - + -
1221J VAL* 3.6 43.9 + - + +
1224J VAL* 5.2 5.4 - - - +
1366J LYS* 3.0 69.1 + - + +
1367J HIS* 3.7 24.5 + - - -
1370J ILE* 4.1 11.2 - - + -
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Residues in contact with GLY1206 (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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1146J GLY 3.1 9.9 - - - -
1148J VAL* 3.9 4.7 - - - +
1165J TYR* 3.5 17.9 - - - -
1202J GLN 2.6 19.2 + - - -
1204J CYS 3.7 0.4 - - - -
1205J TYR* 1.3 74.6 - - - +
1207J TYR* 1.3 68.4 + - - +
1215J VAL* 2.9 27.5 + - - +
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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