Contacts of the strand formed by residues 132 - 140 (chain A) in PDB entry 3OJW
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 LEU 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A MET* 4.9 0.2 - - - +
79A ASN 2.8 8.6 + - - +
80A ILE* 3.4 21.5 - - + +
81A ILE* 3.0 27.0 + - - +
125A LEU* 4.6 3.8 - - - -
131A SER* 1.3 76.2 - - - +
133A VAL* 1.3 64.8 + - - +
134A VAL* 3.8 22.7 - - + -
167A LYS* 3.4 32.3 - - + +
168A PHE* 3.8 15.3 - - - +
169A ALA* 4.8 1.3 - - + -
200A ILE* 4.6 9.9 - - + -
223A PHE* 4.1 4.0 - - + -
227A VAL* 3.9 36.6 - - + -
231A PHE* 3.9 13.5 - - + -
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Residues in contact with VAL 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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81A ILE* 3.4 9.9 - - + +
83A PHE* 3.8 20.2 - - + -
122A LEU* 3.8 22.4 - - + -
125A LEU* 3.6 17.9 - - + +
132A LEU* 1.3 74.2 - - - +
134A VAL* 1.3 63.9 + - - +
135A PHE* 3.4 30.8 - - + -
166A VAL* 4.0 6.7 - - + -
167A LYS 3.0 18.9 + - - +
168A PHE* 3.1 31.6 - - + +
169A ALA 3.3 2.6 + - - +
192A LEU* 5.6 0.7 - - + -
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Residues in contact with VAL 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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80A ILE* 4.7 4.0 - - + -
81A ILE 2.9 8.7 + - - +
82A VAL* 3.2 29.7 - - + +
83A PHE* 2.8 27.0 + - - +
98A LEU* 4.3 17.3 - - + -
132A LEU* 3.8 18.6 - - + -
133A VAL* 1.3 79.7 - - - +
135A PHE* 1.3 72.7 + - - +
169A ALA* 3.3 15.9 - - + +
171A PHE* 5.8 0.2 - - + -
219A TRP* 4.3 12.6 - - + -
223A PHE* 3.7 23.8 - - + -
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Residues in contact with PHE 135 (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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83A PHE* 3.5 35.2 - + + -
119A LEU* 4.2 9.4 - - + -
122A LEU* 4.5 6.3 - - + -
133A VAL* 3.4 34.1 - - + -
134A VAL* 1.3 76.7 - - - +
136A ALA* 1.3 56.2 + - - +
137A MET* 3.8 19.3 - - + -
152A PHE* 3.6 37.7 - + - -
168A PHE* 4.9 0.2 - - + -
169A ALA 3.0 17.2 + - - +
170A VAL* 3.4 10.9 - - + +
171A PHE* 2.8 33.3 + - - +
188A VAL* 4.1 5.4 - - + -
192A LEU* 3.4 31.9 - - + -
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Residues in contact with ALA 136 (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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82A VAL* 4.9 3.7 - - + +
83A PHE 2.9 11.7 + - - +
84A TYR* 3.3 2.4 - - - -
85A GLY 2.8 26.2 + - - +
91A ALA* 3.7 26.0 - - + +
94A PHE* 4.6 6.5 - - + -
95A ALA* 4.5 13.2 - - + +
98A LEU* 5.4 4.3 - - + -
134A VAL 4.3 0.2 - - - -
135A PHE* 1.3 70.3 - - - +
137A MET* 1.3 59.7 + - - +
171A PHE* 3.3 15.3 - - + +
173A LEU* 4.1 8.5 - - + -
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Residues in contact with MET 137 (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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83A PHE* 4.3 3.6 - - - +
84A TYR 4.4 1.1 - - - -
85A GLY* 3.6 14.1 - - - -
114A PRO* 5.5 2.0 - - + -
135A PHE* 3.8 34.1 - - + +
136A ALA* 1.3 86.6 - - - +
138A ALA* 1.3 63.0 + - - +
149A ALA* 3.6 30.5 - - + -
152A PHE* 4.1 20.2 - - + -
170A VAL* 4.9 3.6 - - + -
171A PHE 3.1 8.1 + - - +
172A GLY* 3.4 4.7 - - - -
173A LEU* 2.8 25.7 + - - +
182A ASN* 4.3 1.2 + - - -
184A MET* 4.0 25.4 - - + -
185A GLY* 4.5 10.7 + - - +
188A VAL* 4.5 14.4 - - + -
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Residues in contact with ALA 138 (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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85A GLY* 2.9 19.9 + - - +
91A ALA* 4.6 0.2 - - + -
137A MET* 1.3 73.3 - - - +
139A THR* 1.3 61.3 + - - +
140A TYR* 3.9 5.2 - - + -
145A PRO* 4.4 0.2 - - - +
146A THR* 3.5 23.2 + - + +
173A LEU* 3.3 11.8 - - + +
184A MET* 3.8 12.4 - - - +
751A FMN 3.3 43.5 - - - +
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Residues in contact with THR 139 (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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138A ALA* 1.3 75.5 - - - +
140A TYR* 1.3 67.7 + - - +
143A GLY* 3.4 35.9 - - - +
144A ASP 3.8 2.7 - - - -
173A LEU 3.1 9.5 + - - -
180A HIS 3.8 5.4 - - - +
182A ASN* 3.3 7.4 + - - -
183A ALA 3.3 8.4 + - - +
184A MET* 2.9 24.3 + - - +
185A GLY 4.0 1.2 + - - -
751A FMN 2.7 60.6 + - - +
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Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A GLN* 3.5 34.9 - - + +
88A THR* 3.4 18.6 + - + +
138A ALA* 3.9 7.6 - - + -
139A THR* 1.3 78.2 - - - +
141A GLY* 1.3 69.6 + - - +
142A GLU 3.1 0.3 + - - -
143A GLY 2.8 16.3 + - - -
144A ASP* 2.6 21.1 + - + +
145A PRO 4.3 7.0 - - - +
146A THR* 3.6 26.9 - - + -
751A FMN 2.5 97.4 + + + +
752A FAD 5.1 4.5 - - + -
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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