Contacts of the strand formed by residues 120 - 127 (chain A) in PDB entry 1OY2
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 MET 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.1 2.8 - - - -
56A TYR* 2.7 43.5 + - + +
117A PHE* 4.5 15.5 - - + +
118A ALA 3.1 6.7 - - - +
119A GLY* 1.3 77.3 - - - +
121A PRO* 1.3 63.3 - - + +
122A ILE* 3.4 31.2 + - + +
135A ALA* 4.1 6.1 - - + -
137A ASP* 5.1 10.5 - - - +
138A CYS* 3.9 33.9 - - + +
140A GLN* 5.7 1.1 - - - +
142A ILE* 4.4 8.5 - - + -
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Residues in contact with PRO 121 (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* 4.5 9.2 - - + +
54A VAL 4.2 0.4 - - - +
55A ARG* 3.3 41.5 - - + +
119A GLY 3.6 7.9 - - - +
120A MET* 1.3 83.8 - - + +
122A ILE* 1.3 65.7 + - - +
136A ALA* 3.9 2.8 - - - +
137A ASP* 3.5 33.0 + - + +
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Residues in contact with ILE 122 (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* 3.4 8.2 - - - +
54A VAL 2.8 38.4 + - - +
56A TYR* 4.7 10.5 - - + -
120A MET* 3.4 41.5 + - + +
121A PRO* 1.3 78.9 - - - +
123A THR* 1.3 78.8 + - - +
124A LEU* 3.4 16.4 - - + +
133A LEU* 3.9 18.2 - - + -
134A MET 3.2 10.5 - - - +
135A ALA* 3.5 3.8 - - - -
136A ALA* 3.4 19.1 - - - +
137A ASP 4.3 1.3 - - - +
142A ILE* 4.0 7.9 - - + -
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Residues in contact with THR 123 (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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51A SER* 5.6 3.6 - - - -
52A TYR* 3.3 18.4 - - - +
53A LEU* 3.9 20.2 - - + -
122A ILE* 1.3 70.8 - - - +
124A LEU* 1.3 61.2 + - - +
125A THR* 4.5 1.0 + - - -
134A MET* 2.8 57.8 + - - +
135A ALA 4.6 0.2 - - - -
136A ALA* 3.3 13.2 - - + +
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Residues in contact with LEU 124 (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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50A VAL 3.8 0.5 - - - +
51A SER* 3.1 3.1 - - - -
52A TYR 2.9 30.8 + - - -
54A VAL* 2.9 20.9 - - + -
56A TYR* 5.3 6.7 - - + -
122A ILE* 3.4 11.7 + - + +
123A THR* 1.3 70.7 - - - +
125A THR* 1.3 88.9 + - - +
126A VAL* 4.0 13.2 - - + -
131A LEU* 3.9 28.3 - - + -
133A LEU* 4.2 24.9 - - + +
166A TYR* 5.9 1.6 - - + +
180A LEU* 4.0 28.3 - - + -
186A LEU* 4.1 9.3 - - + +
190A VAL* 6.4 0.7 - - + -
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Residues in contact with THR 125 (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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48A PRO 4.8 2.5 - - - +
49A GLY* 4.2 11.7 - - - +
50A VAL 3.1 11.2 - - - +
51A SER* 2.7 26.3 - - - -
123A THR 4.5 0.7 + - - -
124A LEU* 1.3 75.2 - - - +
126A VAL* 1.3 71.7 + - - +
127A SER* 4.1 4.4 + - - +
131A LEU* 3.7 5.0 - - - +
132A ASN* 3.0 44.0 + - + +
134A MET* 3.8 21.3 - - + +
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Residues in contact with VAL 126 (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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38A TRP* 3.4 38.4 - - + +
45A VAL* 4.0 7.3 - - + +
49A GLY* 3.5 5.9 - - - -
50A VAL* 2.8 55.1 + - + -
124A LEU* 4.0 7.6 - - + -
125A THR* 1.3 75.5 - - - +
127A SER* 1.3 61.2 + - - +
131A LEU* 3.5 19.7 - - + -
166A TYR* 4.8 2.2 - - - +
186A LEU* 3.4 26.2 - - + -
197A ALA* 5.9 0.2 - - + -
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Residues in contact with SER 127 (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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45A VAL* 3.0 24.4 + - - -
47A GLY 5.8 0.2 + - - -
48A PRO 5.4 0.2 - - - -
49A GLY* 4.1 7.3 - - - -
125A THR* 5.1 4.8 - - - +
126A VAL* 1.3 75.7 + - - +
128A THR* 1.3 61.8 + - - +
129A SER 2.8 10.9 + - - -
130A SER* 2.9 35.1 + - - +
131A LEU* 4.4 1.4 - - - +
132A ASN 5.9 0.4 - - - -
149A SER* 4.4 2.9 + - - -
197A ALA* 5.3 2.1 - - - +
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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