Contacts of the strand formed by residues 89 - 97 (chain 7) in PDB entry 4UOW
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 GLY 89 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206 LYS* 4.0 8.1 - - - -
216 VAL* 3.3 17.7 - - - -
97 ALA* 4.6 0.4 - - - -
107 PRO* 3.3 13.8 - - - +
857 ARG* 3.5 1.4 - - - -
867 ASN* 2.9 36.3 + - - +
887 ILE* 1.3 80.4 - - - +
907 GLU* 1.3 62.2 + - - +
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Residues in contact with GLU 90 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156 SER 2.8 27.4 - - - +
166 ILE* 3.5 20.9 - - + +
176 ASP* 3.6 0.2 - - - +
206 LYS* 2.9 22.2 + - - +
216 VAL 2.9 9.8 + - - +
236 THR* 3.0 27.5 + - - -
976 ARG* 4.1 3.4 + - - -
107 PRO* 4.1 4.1 - - - +
837 ARG* 3.8 8.7 - - + -
847 ALA 3.3 4.5 - - - +
857 ARG* 3.0 36.9 + - + -
897 GLY* 1.3 78.7 - - - +
917 ALA* 1.3 59.9 + - - +
927 PHE* 3.2 24.3 - - + -
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Residues in contact with ALA 91 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236 THR* 3.6 13.7 - - + -
107 PRO* 3.4 33.2 - - + +
117 ARG* 4.2 0.4 - - - +
127 PHE* 3.5 24.5 - - + -
837 ARG* 3.5 4.2 - - - +
847 ALA* 2.8 39.6 + - + +
907 GLU* 1.3 72.7 - - - +
927 PHE* 1.3 63.6 + - - +
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Residues in contact with PHE 92 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116 PRO* 4.5 9.2 - - + -
136 ASP 5.5 0.2 - - - -
146 ILE* 3.6 42.2 - - + -
156 SER 3.9 7.9 - - - -
226 LEU* 3.6 24.9 - - + -
236 THR* 2.8 19.8 + - - +
246 VAL* 4.6 6.1 - - + -
256 ALA* 2.9 28.9 + - - +
127 PHE* 3.8 3.0 - - - -
447 GLU* 5.7 4.3 - - - -
817 VAL* 3.9 17.9 - - + -
827 CYS 3.4 2.0 - - - -
837 ARG* 3.5 31.2 - - + -
907 GLU* 3.2 33.2 - - + -
917 ALA* 1.3 76.5 - - - +
937 ALA* 1.3 61.1 + - - +
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Residues in contact with ALA 93 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116 PRO* 5.2 1.5 - - - +
256 ALA* 3.7 19.1 - - + +
127 PHE* 3.7 22.9 - - + -
157 ARG* 5.0 3.8 - - + -
167 PRO* 3.5 25.5 - - + +
817 VAL* 3.7 3.1 - - - -
827 CYS* 2.8 33.0 + - - +
927 PHE* 1.3 76.9 - - - +
947 ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 94 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 ALA* 3.6 36.2 + - + +
116 PRO* 4.3 7.2 - - + +
256 ALA 4.2 6.1 + - - -
157 ARG* 5.2 6.9 + - - +
167 PRO* 4.4 9.6 - - - +
797 GLN* 4.4 4.5 - - + -
807 TYR 3.2 13.0 - - - +
817 VAL* 3.7 18.6 - - + -
937 ALA* 1.3 76.0 - - - +
957 VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 95 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96 ALA* 4.0 6.5 - - - -
157 ARG* 5.1 6.5 - - - +
167 PRO* 3.4 40.6 - - + +
177 LYS* 4.6 0.7 - - - -
187 ALA* 4.4 16.8 - - + +
297 LEU* 3.8 31.4 - - + -
437 TRP* 4.9 0.4 - - + -
807 TYR* 2.8 42.2 + - - +
947 ALA* 1.3 76.1 - - - +
967 GLY* 1.3 72.1 + - - +
977 LEU* 3.7 1.4 + - + +
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Residues in contact with GLY 96 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86 GLU 5.3 2.4 + - - -
96 ALA* 4.0 11.8 - - - +
187 ALA* 5.5 1.6 - - - +
787 GLY 3.7 6.5 - - - -
797 GLN* 4.4 7.2 - - - -
957 VAL* 1.3 81.3 - - - +
977 LEU* 1.3 61.1 + - - -
987 GLN* 4.0 3.1 + - - +
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Residues in contact with LEU 97 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187 ALA* 3.8 21.8 - - + -
207 VAL* 3.8 29.4 - - + -
277 ALA* 5.3 0.9 - - + -
297 LEU* 4.2 8.1 - - + -
697 ILE* 3.8 24.9 - - + -
727 LEU* 4.0 17.7 - - + -
767 ASP 3.5 22.2 - - - +
777 SER* 3.2 4.3 - - - -
787 GLY* 2.9 32.1 + - - +
807 TYR* 3.7 17.7 - - + -
957 VAL* 3.7 1.4 + - + -
967 GLY* 1.3 72.7 - - - -
987 GLN* 1.3 63.8 + - - +
997 VAL* 4.1 7.0 - - + -
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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