Contacts of the strand formed by residues 1108 - 1116 (chain A) in PDB entry 3PLS
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 ARG1108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1081A VAL* 6.2 0.8 - - - +
1100A GLU* 3.1 42.0 + - + +
1101A TYR 3.5 7.2 - - - +
1102A ILE* 4.5 13.6 - - + +
1106A GLN 5.9 0.7 - - - -
1107A ASN* 1.3 74.9 - - - +
1109A ILE* 1.3 65.2 + - - +
1110A GLN* 4.3 0.9 + - - +
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Residues in contact with ILE1109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100A GLU* 3.3 4.1 - - - -
1101A TYR* 2.8 59.5 + - + +
1103A ASP* 3.0 42.0 - - - +
1107A ASN* 4.4 7.0 - - + +
1108A ARG* 1.3 79.9 - - - +
1110A GLN* 1.3 72.9 + - - +
1111A CYS* 5.2 0.9 - - + -
1147A ILE* 5.8 0.9 - - + -
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Residues in contact with GLN1110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083A HIS* 3.3 23.2 + - - -
1086A ARG* 3.8 19.9 + - - +
1098A HIS* 4.8 4.2 + - - +
1099A GLY 2.9 25.4 + - - +
1100A GLU* 3.0 28.2 + - - +
1108A ARG 4.2 1.2 + - - +
1109A ILE* 1.3 82.2 - - - +
1111A CYS* 1.3 64.7 + - - +
1162A PRO* 5.8 0.2 - - - +
1163A TYR* 4.8 6.7 + - + +
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Residues in contact with CYS1111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098A HIS* 3.7 6.6 + - - +
1099A GLY 2.8 34.5 + - - +
1100A GLU 4.5 1.6 - - - -
1101A TYR* 3.8 26.5 - - + -
1109A ILE* 5.2 0.7 - - + -
1110A GLN* 1.3 77.7 - - - +
1112A ALA* 1.3 69.9 + - - +
1113A ILE* 4.1 13.2 - - - -
1147A ILE* 3.9 15.9 - - + -
1160A LEU* 4.4 7.0 - - - -
1161A LEU 3.2 12.8 - - - +
1162A PRO* 4.5 0.9 - - + -
1163A TYR* 4.0 19.0 - - - +
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Residues in contact with ALA1112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088A ILE* 4.0 9.2 - - + -
1096A VAL* 4.0 13.7 - - + -
1097A TYR 3.4 9.4 - - - +
1111A CYS* 1.3 75.0 - - - +
1113A ILE* 1.3 67.8 + - - +
1114A LYS 4.4 0.2 - - - -
1159A VAL 4.4 0.2 - - - -
1160A LEU* 3.5 1.4 - - - -
1161A LEU* 2.9 34.9 + - + +
1163A TYR* 4.0 3.6 - - + +
1358A ANP 3.8 35.2 - - + +
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Residues in contact with ILE1113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080A VAL* 3.5 31.0 - - + -
1081A VAL 3.8 2.5 - - - +
1082A THR* 3.7 21.1 - - + +
1095A VAL 3.5 1.9 - - - +
1096A VAL* 3.1 2.8 - - - -
1097A TYR* 2.7 43.6 + - - +
1099A GLY* 3.8 26.7 - - - -
1100A GLU 4.1 3.6 - - - +
1111A CYS* 4.1 6.7 - - - -
1112A ALA* 1.3 81.5 - - - +
1114A LYS* 1.3 61.2 + - - +
1115A SER 4.0 0.2 - - - -
1158A HIS* 3.8 35.7 - - + -
1159A VAL 3.3 6.3 - - - +
1160A LEU* 4.1 13.9 - - + -
1161A LEU* 5.4 0.2 - - - -
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Residues in contact with LYS1114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093A PHE* 5.0 3.4 - - - +
1094A GLY* 4.4 14.8 - - - +
1095A VAL 3.2 11.4 - - - +
1096A VAL* 4.1 9.0 - - + +
1113A ILE* 1.3 73.1 - - - +
1115A SER* 1.3 68.2 + - - +
1116A LEU* 3.5 22.4 + - + +
1158A HIS* 3.2 4.8 - - - -
1159A VAL* 2.8 44.2 + - + +
1161A LEU* 4.3 17.0 - - + +
1226A ASP* 3.1 28.6 + - - +
1229A LEU* 4.3 17.2 - - + +
1358A ANP 3.2 46.9 + - - -
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Residues in contact with SER1115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094A GLY* 2.9 24.8 - - - -
1095A VAL* 2.8 28.3 + - - +
1097A TYR* 4.2 11.5 + - - -
1113A ILE 4.0 1.4 + - - -
1114A LYS* 1.3 71.7 - - - +
1116A LEU* 1.3 58.3 + - - +
1117A SER* 3.4 1.6 + - - -
1156A LEU* 3.6 23.3 - - - +
1157A PRO 3.8 5.2 - - - -
1158A HIS* 3.6 25.9 - - - -
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Residues in contact with LEU1116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093A PHE* 3.5 8.7 - - + +
1114A LYS* 3.6 32.3 - - + +
1115A SER* 1.3 69.6 - - - +
1117A SER* 1.3 63.2 + - - +
1118A ARG 3.3 2.7 + - - -
1119A ILE* 3.7 29.0 + - + -
1128A PHE* 3.3 41.3 - - + -
1156A LEU* 3.5 19.6 - - - +
1157A PRO* 2.8 30.1 + - + +
1159A VAL* 3.5 15.9 - - + -
1229A LEU* 4.3 17.3 - - + -
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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