Contacts of the strand formed by residues 1107 - 1111 (chain A) in PDB entry 4I51
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 TRP1107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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979A VAL* 4.7 0.4 - - + -
994A CYS* 3.4 29.8 - - - -
995A VAL 3.6 15.0 - - - -
996A ASN* 3.9 20.0 - - + -
1001A GLU* 3.9 12.1 - - + +
1002A PRO 3.3 27.6 - - - -
1004A PRO* 3.6 27.3 - - + +
1099A LEU* 3.8 7.9 - - + -
1100A TYR 3.4 24.7 - - - -
1101A ARG* 3.1 38.4 - - + +
1102A THR* 4.0 0.2 - - - -
1106A GLY* 1.3 72.7 - - - -
1108A GLY* 1.3 58.4 + - - +
1167A PHE* 3.5 32.7 - + + +
1169A ASN* 3.1 9.4 + - - -
3001A SAH 2.8 39.1 + - - +
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Residues in contact with GLY1108 (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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1099A LEU* 3.4 8.1 - - - +
1100A TYR* 2.8 36.0 + - - -
1102A THR* 3.6 7.5 - - - +
1107A TRP* 1.3 74.0 - - - +
1109A VAL* 1.3 64.3 + - - -
1167A PHE 3.5 8.5 - - - -
1169A ASN* 3.6 12.3 - - - -
1206A GLN* 3.8 6.7 - - - -
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Residues in contact with VAL1109 (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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1097A LEU* 4.1 9.6 - - + -
1098A GLN 3.4 9.9 - - - +
1099A LEU* 4.4 2.9 - - + -
1100A TYR* 3.7 2.6 - - - -
1108A GLY* 1.3 77.8 - - - +
1110A ARG* 1.3 61.9 + - - +
1164A VAL* 3.6 44.4 - - + +
1167A PHE* 3.7 16.4 + - + -
1168A ILE* 3.8 22.6 - - + +
1206A GLN* 3.4 7.6 + - - +
1207A LEU* 2.7 51.8 + - + +
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Residues in contact with ARG1110 (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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976A GLU* 4.4 8.1 + - - -
995A VAL* 4.2 5.5 - - - +
1097A LEU* 3.4 8.4 - - - +
1098A GLN* 2.7 79.7 + - + +
1100A TYR* 3.4 54.5 - - + +
1109A VAL* 1.3 76.6 - - - +
1111A SER* 1.3 66.3 + - - +
1112A LEU* 4.2 7.2 - - - -
1204A GLY* 3.3 25.6 + - - +
1205A GLU 3.3 15.7 - - - +
1206A GLN* 4.2 0.2 - - - -
1207A LEU* 4.2 2.5 - - - +
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Residues in contact with SER1111 (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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1095A ALA* 5.3 0.3 - - - +
1096A ARG 3.7 8.1 + - - -
1097A LEU* 4.0 5.8 - - - +
1110A ARG* 1.3 77.4 - - - +
1112A LEU* 1.3 60.5 + - - +
1113A GLN* 2.5 31.3 + - - +
1115A ILE* 3.3 28.2 - - - +
1201A ILE* 4.3 15.9 - - - -
1202A GLU 4.6 1.8 - - - -
1204A GLY* 2.8 28.9 + - - -
1205A GLU 3.1 7.0 + - - -
1207A LEU* 4.5 3.7 - - - +
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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