Contacts of the strand formed by residues 1111 - 1116 (chain A) in PDB entry 1NDX
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 PRO1111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1067A ARG* 4.5 0.2 - - - +
1081A THR* 3.8 13.4 - - + +
1082A ASP 3.1 29.8 - - - +
1083A TRP* 3.3 30.3 + - - +
1088A PRO* 3.6 8.5 - - + -
1089A LYS 3.9 0.4 - - - +
1107A ASP* 3.0 16.5 - - - +
1110A LEU* 1.3 82.1 - - - +
1112A ASN* 1.3 63.8 + - - +
1125A TRP* 3.5 39.3 - - + -
1126A VAL 3.4 8.7 - - - +
1127A ASP* 4.0 5.8 - - - +
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Residues in contact with ASN1112 (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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1024A GLU* 4.9 1.1 - - - -
1067A ARG* 3.4 29.7 - - + +
1068A GLY 3.0 15.6 + - - -
1081A THR* 2.8 20.7 + - - -
1083A TRP* 4.1 6.1 - - - +
1110A LEU* 3.8 9.3 + - - +
1111A PRO* 1.3 80.6 + - - +
1113A GLY* 1.3 61.6 + - - +
1126A VAL 2.9 9.7 + - - +
1128A ALA* 3.2 23.9 - - - +
1152A TYR* 4.2 1.2 - - - -
1153A PRO 3.9 5.4 - - - +
1154A PHE* 3.0 48.2 - - + +
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Residues in contact with GLY1113 (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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1024A GLU* 5.8 0.4 - - - -
1068A GLY* 4.5 6.5 - - - -
1112A ASN* 1.3 80.5 + - - +
1114A LEU* 1.3 61.4 + - - +
1125A TRP* 3.5 2.6 - - - +
1126A VAL* 3.0 33.1 + - - +
1154A PHE 3.1 11.8 + - - -
1155A ALA* 3.7 14.1 - - - -
1156A VAL* 3.4 6.6 - - - +
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Residues in contact with LEU1114 (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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1068A GLY* 4.7 6.1 - - - +
1069A ILE 4.6 2.8 + - - -
1070A VAL* 3.2 23.0 + - + +
1079A TYR* 3.4 44.0 - - + +
1080A TRP 4.1 0.4 - - - -
1081A THR* 3.4 19.7 + - + +
1090A ILE* 3.5 22.2 - - + -
1113A GLY* 1.3 75.5 - - - +
1115A HIS* 1.3 69.2 + - - +
1123A LEU* 3.9 17.3 - - + +
1124A CYS 3.5 13.7 - - - +
1125A TRP* 3.5 21.8 - - + -
1156A VAL* 4.0 6.2 + - - +
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Residues in contact with HIS1115 (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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1070A VAL* 3.7 13.2 - - + -
1114A LEU* 1.3 75.2 - - - +
1116A PHE* 1.3 65.8 + - - +
1117A ASP* 4.0 6.6 + - - +
1122A GLN 5.1 0.4 + - - -
1123A LEU* 3.3 6.6 - - - -
1124A CYS* 3.0 57.1 + - + +
1156A VAL* 3.2 28.9 + - + +
1157A THR* 3.6 9.6 - - - -
1158A SER* 3.3 40.0 + - - +
1162A ASN 5.4 0.8 + - - -
1163A LEU* 3.2 35.1 - - + +
1178A LEU* 5.2 4.9 - - - +
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Residues in contact with PHE1116 (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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1070A VAL* 3.4 12.1 - - + +
1071A THR 3.5 19.4 - - - +
1072A ASP* 3.5 36.3 - - + -
1073A SER 5.8 0.7 + - - -
1077A ASN* 4.4 7.6 - - + -
1079A TYR* 3.3 42.6 - + + -
1115A HIS* 1.3 76.2 - - - +
1117A ASP* 1.3 73.8 + - - +
1120A SER* 3.4 29.8 - - - -
1121A SER* 3.5 9.6 - - - -
1122A GLN 3.3 17.0 - - - -
1123A LEU* 3.5 13.7 - - + -
1138A PRO* 4.6 6.3 - - + -
1158A SER* 3.4 14.0 + - - -
1159A TYR* 5.8 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