Contacts of the strand formed by residues 129 - 134 (chain A) in PDB entry 3ORH
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 PHE 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ARG* 3.6 19.5 - - + +
65A LEU* 3.7 24.9 - - + -
87A TRP* 3.5 57.0 - + - -
124A LEU* 4.1 22.4 - - + -
125A PRO* 4.2 8.7 - - + -
127A GLY 3.7 0.2 - - - -
128A HIS* 1.3 98.1 - + + +
130A ASP* 1.3 62.7 + - - +
131A GLY 3.4 10.8 - - - +
132A ILE* 4.3 9.2 - - + -
159A LEU* 3.1 28.2 + - + +
160A LEU* 3.4 6.4 - - - +
161A LYS* 2.9 29.9 + - - -
164A GLY* 4.5 0.2 - - - -
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Residues in contact with ASP 130 (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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57A ALA 4.8 0.2 - - - -
60A LYS* 3.9 21.1 - - + +
61A GLY 3.4 20.0 - - - +
62A GLY* 3.5 9.2 - - - -
63A ARG* 2.8 29.9 + - - +
129A PHE* 1.3 72.8 - - - +
131A GLY* 1.3 57.1 + - - +
160A LEU* 4.3 0.2 - - - -
161A LYS* 3.3 38.8 + - - +
164A GLY* 3.3 8.2 - - - -
165A VAL* 2.9 27.9 + - - +
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Residues in contact with GLY 131 (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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57A ALA 3.3 22.2 - - - -
63A ARG 3.3 5.2 + - - +
64A VAL* 3.4 5.4 - - - +
65A LEU 2.9 24.8 + - - -
129A PHE* 3.4 2.9 - - - +
130A ASP* 1.3 82.7 - - - +
132A ILE* 1.3 67.4 + - - +
160A LEU* 4.2 0.2 - - - -
165A VAL* 3.2 10.5 - - - -
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Residues in contact with ILE 132 (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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57A ALA* 3.8 5.3 - - - +
65A LEU* 3.3 26.9 - - + +
67A VAL* 4.8 1.1 - - + -
129A PHE* 4.3 3.8 - - + -
131A GLY* 1.3 77.9 - - - +
133A LEU* 1.4 68.5 + - - +
151A PHE* 3.9 20.6 - - + -
156A ALA* 3.8 34.8 - - + +
159A LEU* 3.9 19.3 - - + -
160A LEU* 3.8 17.9 - - + -
165A VAL 2.9 8.6 + - - +
166A LEU* 3.6 20.8 - - + -
167A THR* 2.9 30.9 + - - +
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Residues in contact with LEU 133 (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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53A LEU* 3.8 15.3 - - + +
54A ALA* 3.7 35.2 - - - +
57A ALA* 3.8 10.3 - - + +
64A VAL* 5.4 1.6 - - + -
65A LEU 2.8 11.7 + - - +
66A GLU* 3.4 17.0 - - + +
67A VAL* 2.8 28.1 + - - +
68A GLY 6.0 0.2 - - - +
74A ALA* 3.8 22.7 - - + -
78A VAL* 4.4 7.9 - - + -
132A ILE* 1.4 74.4 - - - +
134A TYR* 1.4 62.9 + - - +
135A ASP* 3.9 24.2 - - + +
167A THR* 3.5 15.5 - - + +
168A TYR* 5.5 0.2 - - - -
4000A SAH 5.0 1.3 - - - +
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Residues in contact with TYR 134 (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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67A VAL* 3.9 13.9 - - + -
117A TRP* 2.9 39.0 + + - -
132A ILE 4.1 0.6 - - - -
133A LEU* 1.4 70.3 - - - +
135A ASP* 1.3 61.4 + - - +
136A THR* 2.9 16.2 + - + -
147A HIS* 2.7 45.0 + + - -
148A GLN* 3.6 28.0 - - + -
151A PHE* 3.4 45.3 - + + -
152A ILE* 5.8 0.9 - - + -
166A LEU* 4.8 3.4 - - + -
167A THR 3.0 9.2 + - - +
168A TYR* 3.1 34.3 - - + +
169A CYS 3.2 10.4 + - - -
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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