Contacts of the strand formed by residues 113 - 119 (chain D) in PDB entry 3OP5
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 TYR 113 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D MET* 4.8 2.9 - - - -
84D LEU* 3.6 24.4 - - + +
87D TYR* 3.8 36.3 - - + -
88D GLN* 4.0 21.7 + - + -
91D ALA 3.9 14.5 + - - +
92D LYS* 5.5 5.4 - - + -
93D PRO* 3.8 25.5 - - + +
111D PRO 3.8 2.4 + - - -
112D LYS* 1.3 72.1 - - - +
114D TRP* 1.4 58.8 + - - +
115D GLY* 3.4 29.4 - - - -
116D SER* 2.9 23.4 + - - -
129D MET* 4.3 1.1 - - + -
131D MET* 3.4 24.2 - - + -
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Residues in contact with TRP 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ASP* 4.3 2.9 - - - +
37D TRP* 3.8 27.4 - + + -
56D MET* 4.9 10.5 - - + -
67D PRO* 5.3 6.7 - - + -
68D CYS* 3.8 21.6 - - - -
112D LYS* 3.4 56.6 - - + +
113D TYR* 1.4 73.9 - - - +
115D GLY* 1.3 57.8 + - - +
130D ILE* 2.8 25.4 + - + +
131D MET 3.8 16.6 - - - -
132D ASP* 2.9 26.8 + - - +
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Residues in contact with GLY 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ASP* 3.9 13.7 - - - -
113D TYR* 3.4 22.3 - - - -
114D TRP* 1.3 80.4 - - - +
116D SER* 1.4 59.3 + - - -
129D MET* 3.6 0.3 - - - -
130D ILE* 2.7 37.7 + - - +
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Residues in contact with SER 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ASP* 3.1 10.1 - - - +
32D MET* 2.8 51.1 + - - +
84D LEU* 3.7 28.9 - - - +
88D GLN* 4.8 0.3 + - - -
113D TYR* 2.9 19.8 + - - -
115D GLY* 1.4 74.7 - - - -
117D GLY* 1.3 52.8 + - - +
128D PHE* 3.4 22.7 - - - -
129D MET* 4.2 0.9 - - - -
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Residues in contact with GLY 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D THR 4.8 0.4 - - - -
31D ASP* 4.5 1.1 - - - -
32D MET* 4.2 15.5 - - - -
116D SER* 1.3 79.1 + - - +
118D LEU* 1.3 63.6 + - - +
127D ARG* 3.6 7.6 - - - +
128D PHE* 3.1 42.7 + - - +
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D THR 4.4 5.7 + - - +
75D SER 3.4 26.0 - - - +
117D GLY* 1.3 75.5 - - - +
119D HIS* 1.3 63.6 + - - +
125D SER* 4.5 11.4 - - - +
126D TYR 3.4 5.8 - - - +
127D ARG* 3.7 39.9 - - + +
128D PHE* 3.6 7.9 - - - -
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Residues in contact with HIS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLU* 4.7 12.4 - - + +
28D ILE 3.9 14.6 - - - -
29D ILE* 3.5 34.6 - - + +
30D THR 5.0 2.2 + - - -
72D VAL* 6.4 0.7 - - + -
118D LEU* 1.3 77.5 + - - +
120D ASP* 1.3 83.8 + - - +
124D LYS 3.3 4.0 - - - +
125D SER* 3.3 4.4 - - - -
126D TYR* 2.8 42.5 + - + +
128D PHE* 4.4 10.7 - - + -
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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