Contacts of the strand formed by residues 99 - 105 (chain A) in PDB entry 1O94
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.5 1.8 - - + -
18A LYS* 3.9 29.6 - - + +
19A THR 3.7 25.8 - - - +
20A LEU* 3.9 19.5 - - + -
54A ALA 2.9 15.7 + - - +
55A ALA* 3.2 1.8 - - + -
56A LEU 2.8 25.5 + - - -
93A VAL* 3.5 5.2 - - - +
94A HIS* 5.7 0.7 - - + -
97A GLY 5.8 0.4 - - - +
98A ALA* 1.3 77.4 - - - +
100A ALA* 1.3 60.8 + - - +
164A ASP* 3.5 26.9 - - + +
165A ILE* 4.0 19.7 - - + -
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Residues in contact with ALA 100 (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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56A LEU 3.3 5.6 - - - +
89A MET* 4.2 5.8 - - - -
90A THR* 3.8 36.1 - - + -
93A VAL* 3.9 16.1 - - + +
94A HIS* 4.2 2.0 - - - +
99A LEU* 1.3 75.4 - - - +
101A GLY* 1.3 59.1 + - - +
163A PHE* 3.6 4.3 - - + -
164A ASP* 2.7 41.6 + - - +
165A ILE* 3.1 6.6 + - - -
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Residues in contact with GLY 101 (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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56A LEU 2.8 12.6 + - - +
57A ASN* 3.0 20.5 + - - -
58A THR 2.8 24.9 + - - -
89A MET* 4.4 0.2 - - - +
100A ALA* 1.3 74.6 - - - +
102A VAL* 1.3 58.0 + - - -
163A PHE* 3.3 13.4 - - - -
165A ILE* 3.2 19.1 - - - +
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Residues in contact with VAL 102 (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 ASN* 4.5 0.7 - - - -
58A THR* 3.6 12.6 - - + +
61A CYS* 3.5 32.5 - - + -
77A ILE* 5.3 0.9 - - + -
86A LEU* 5.0 0.7 - - + -
101A GLY* 1.3 75.2 - - - +
103A GLU* 1.3 64.0 + - - +
104A LEU* 3.8 8.5 + - + -
158A SER* 3.3 37.5 - - - +
163A PHE* 3.7 22.2 - - + -
165A ILE 2.9 16.3 + - - +
166A VAL* 3.9 7.0 - - + -
167A TYR* 3.1 29.8 + - - -
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Residues in contact with GLU 103 (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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28A PRO* 3.3 33.7 - - + +
58A THR* 3.5 5.8 + - - +
59A GLU 3.8 7.4 - - - +
60A TYR* 3.1 16.8 + - - +
61A CYS* 2.8 31.1 + - - +
102A VAL* 1.3 77.5 - - - +
104A LEU* 1.3 58.3 + - - +
105A TRP* 4.0 0.2 - - - +
167A TYR* 3.9 11.4 - - + -
169A TYR* 3.3 34.9 - - + -
222A ARG* 3.7 6.4 - - - +
1730A FMN 2.5 43.0 + - - +
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Residues in contact with LEU 104 (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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61A CYS 3.6 2.7 - - - +
63A ILE* 3.8 9.6 - - + -
77A ILE* 4.2 11.2 - - + -
102A VAL* 3.8 11.0 + - + +
103A GLU* 1.3 67.7 - - - +
105A TRP* 1.3 59.3 + - - +
106A TYR 4.3 0.2 + - - -
151A TYR* 3.8 44.3 - - + +
154A ALA* 3.8 17.7 - - + -
155A ALA* 4.0 8.1 - - + +
158A SER* 3.7 20.9 - - - +
166A VAL* 3.6 24.2 - - + -
167A TYR 3.2 19.2 + - - +
168A VAL* 5.7 0.4 - - + -
169A TYR* 3.2 26.3 + - - +
209A VAL* 4.7 5.6 - - + -
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Residues in contact with TRP 105 (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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60A TYR* 3.5 27.1 - + + -
61A CYS 2.8 25.9 + - - +
62A SER* 3.5 21.0 - - - -
63A ILE* 3.1 28.2 + - - +
67A SER* 3.4 34.4 + - - -
69A ASP* 3.5 37.0 - - + -
74A SER* 3.8 15.7 - - - -
103A GLU 4.0 1.3 - - - +
104A LEU* 1.3 74.8 - - - +
106A TYR* 1.3 70.4 + - - +
107A GLY* 3.5 16.3 - - - -
111A ALA* 3.8 11.7 - - + -
151A TYR* 4.6 0.7 - - - -
169A TYR* 3.7 13.0 - + + -
174A TYR* 3.1 52.5 - + + -
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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