Contacts of the strand formed by residues 1004 - 1009 (chain A) in PDB entry 4UI2
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 ILE1004 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994A VAL* 4.0 5.2 - - + -
995A VAL 3.5 8.5 - - - +
996A SER* 4.2 4.7 - - - +
997A LYS 4.4 0.4 - - - +
1001A PRO 4.7 0.7 - - - +
1002A ARG 4.3 0.4 + - - -
1003A THR* 1.3 80.6 - - - +
1005A ILE* 1.3 66.5 + - - +
1006A VAL* 3.8 17.0 - - + -
1049A GLN* 3.6 3.8 - - - -
1050A ILE* 3.0 41.6 + - + +
1053A LEU* 3.3 29.2 - - + -
1059A TYR* 6.0 0.4 - - + -
1061A PHE* 3.5 34.5 - - + -
1080A PHE* 3.7 29.8 - - + -
1082A THR* 4.2 12.6 - - + -
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Residues in contact with ILE1005 (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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993A THR 3.8 0.5 - - - +
994A VAL* 3.5 6.8 - - - +
995A VAL* 2.8 43.1 + - + +
997A LYS* 3.9 32.5 - - + -
1004A ILE* 1.3 75.6 - - - +
1006A VAL* 1.3 65.0 + - - +
1007A ASN* 3.6 25.6 - - - +
1047A THR* 3.6 11.0 - - - +
1048A HIS 3.6 3.8 - - - +
1049A GLN* 3.6 32.3 - - + +
309D LEU* 3.7 32.5 - - + -
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Residues in contact with VAL1006 (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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992A VAL* 4.4 7.9 - - + -
993A THR 3.6 5.4 - - - +
994A VAL* 4.4 6.7 - - + -
1004A ILE* 3.8 20.6 - - + -
1005A ILE* 1.3 75.8 - - - +
1007A ASN* 1.3 66.7 + - - +
1008A TRP* 3.4 22.7 - - + -
1023A ILE* 4.7 12.1 - - + -
1047A THR* 3.1 5.7 + - - -
1048A HIS 2.8 40.5 + - - +
1050A ILE* 4.2 15.7 - - + -
1061A PHE* 4.5 12.3 - - + -
1063A ILE* 3.9 18.2 - - + -
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Residues in contact with ASN1007 (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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992A VAL* 3.5 0.7 - - - -
993A THR* 2.7 47.8 + - - +
995A VAL* 4.7 5.3 - - - +
1005A ILE* 3.6 13.6 - - - +
1006A VAL* 1.3 75.0 - - - +
1008A TRP* 1.3 64.1 + - - +
1046A LEU 3.3 4.3 - - - -
1047A THR* 2.6 32.9 + - - -
186D ALA* 2.9 34.4 + - - +
187D TRP* 4.2 14.1 - - - -
188D PRO* 3.5 17.5 - - - +
198D GLN* 3.7 5.4 - - - +
309D LEU* 4.6 0.2 - - - +
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Residues in contact with TRP1008 (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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989A PRO* 3.9 13.9 - - + -
990A LYS 3.7 8.5 - - - +
991A ASP 3.6 9.0 - - - -
992A VAL* 4.1 5.8 - - + -
1006A VAL* 3.4 33.0 - - + -
1007A ASN* 1.3 82.0 - - - +
1009A GLN* 1.3 75.9 + - - +
1021A TYR* 3.4 39.8 - + + -
1023A ILE* 4.3 8.1 - - + -
1041A VAL* 4.0 17.5 - - + -
1045A ARG 3.2 25.4 - - - -
1046A LEU* 2.9 56.0 + - + +
1047A THR* 3.8 4.0 - - - -
1048A HIS* 3.8 15.3 - - + -
1063A ILE* 3.6 21.3 - - + -
186D ALA* 3.8 1.5 - - - +
198D GLN* 3.5 12.6 + - - +
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Residues in contact with GLN1009 (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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989A PRO* 3.6 4.2 - - - +
990A LYS 2.8 36.8 + - - +
991A ASP* 3.6 13.9 - - + +
1008A TRP* 1.3 84.4 - - - +
1010A PRO* 1.4 75.9 - - + +
1046A LEU* 4.2 0.9 - - - -
186D ALA* 4.5 2.2 - - + -
198D GLN* 3.3 35.6 + - - +
199D VAL 3.6 1.4 - - - +
200D THR* 3.1 38.1 + - - +
215D LYS* 3.5 21.2 - - + +
217D THR* 2.7 26.7 + - - -
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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