Contacts of the strand formed by residues 112 - 121 (chain A) in PDB entry 3O7O
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ILE* 3.6 27.8 - - + -
106A HIS* 4.1 13.5 - - + -
110A LEU* 3.1 20.2 + - + +
111A PRO* 1.3 75.3 - - - +
113A ASN* 1.3 74.4 + - - +
141A TYR* 3.9 14.4 - - + -
142A PHE* 3.3 1.7 - - - +
143A ASN* 2.6 44.3 + - + +
145A LEU* 3.9 7.7 - - - +
231A THR* 4.5 4.0 - - + -
232A GLU 3.3 12.6 - - - +
233A PHE* 4.4 3.8 - - + -
243A PHE* 3.6 38.8 - - + -
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Residues in contact with ASN 113 (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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112A LEU* 1.3 81.5 - - - +
114A PHE* 1.3 59.1 + - - +
115A ALA* 3.4 17.7 + - - +
139A TRP* 3.2 41.4 - - + -
141A TYR 3.3 15.3 - - - +
142A PHE* 4.0 0.9 - - - +
145A LEU* 3.8 3.7 - - + +
231A THR* 3.2 24.1 - - - +
232A GLU* 2.7 55.4 + - - +
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Residues in contact with PHE 114 (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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100A VAL* 4.3 2.9 - - + -
102A PHE* 3.6 44.2 - + + -
104A ILE* 4.1 19.3 - - + -
113A ASN* 1.3 71.9 - - - +
115A ALA* 1.3 57.7 + - - +
116A MET* 3.5 32.5 - - + -
138A VAL 4.0 0.2 - - - +
139A TRP* 3.4 2.3 - - - -
140A PHE* 2.9 52.1 + + + +
141A TYR* 2.9 23.9 + - + -
229A ILE* 3.8 13.5 - - + -
230A GLY 3.5 11.4 - - - -
231A THR* 4.2 0.7 - - - -
247A PHE* 3.3 38.4 - + - -
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Residues in contact with ALA 115 (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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66A TYR* 2.8 24.0 + - + -
113A ASN* 3.4 20.9 + - - +
114A PHE* 1.3 73.4 - - - +
116A MET* 1.3 58.0 + - - +
137A MET* 3.7 19.1 - - + -
138A VAL 3.3 3.8 - - - -
139A TRP* 3.6 26.9 - - + -
230A GLY 3.0 23.1 + - - +
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Residues in contact with MET 116 (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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98A VAL* 4.5 1.3 - - - -
100A VAL* 4.0 17.0 - - + -
114A PHE* 3.5 31.0 - - + -
115A ALA* 1.3 78.0 - - - +
117A GLU* 1.3 65.3 + - - +
137A MET* 3.2 1.9 - - - +
138A VAL* 2.7 38.1 + - + +
140A PHE* 3.8 24.5 - - + -
195A VAL* 4.4 1.8 - - + -
197A PHE* 3.6 21.1 - - + -
227A TRP* 3.4 32.5 - - + -
228A GLU 3.0 8.5 - - - +
229A ILE* 3.8 23.3 - - + -
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Residues in contact with GLU 117 (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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66A TYR* 3.9 19.4 - - - +
116A MET* 1.3 77.8 - - - +
118A THR* 1.4 61.0 + - - +
119A TRP* 3.5 16.1 + - - -
135A GLU* 2.6 35.7 - - - +
136A ILE 3.2 11.9 - - - +
137A MET* 3.4 22.4 - - + +
226A VAL 3.7 0.2 - - - +
227A TRP* 3.4 12.8 - - - -
228A GLU* 2.6 74.3 + - - +
232A GLU* 5.7 0.2 - - - +
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Residues in contact with THR 118 (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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117A GLU* 1.4 73.5 - - - +
119A TRP* 1.3 75.5 + - - +
120A LEU* 3.8 16.3 - - + +
135A GLU* 3.5 7.1 - - - +
136A ILE* 3.0 52.3 + - + +
203A LEU* 4.5 2.5 - - + -
224A PHE* 3.4 31.5 - - + -
226A VAL* 2.6 29.6 + - - -
227A TRP* 3.7 7.9 - - + -
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Residues in contact with TRP 119 (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 ARG* 6.0 0.2 - - - -
74A LYS* 5.2 3.3 - - + +
75A PRO* 4.0 22.2 - - + -
76A TRP* 3.2 36.7 - + - -
117A GLU* 3.5 10.0 + - - -
118A THR* 1.3 76.2 + - - +
120A LEU* 1.3 61.8 + - - +
121A THR* 3.8 4.3 - - + -
129A ALA* 3.7 15.9 - - + -
133A ASP* 6.1 0.2 - - + -
134A VAL 3.4 7.0 - - - -
135A GLU* 3.4 44.9 - - + -
179A TRP* 3.4 38.4 - + - -
223A TYR 3.4 8.0 - - - +
225A THR* 2.6 37.5 + - - +
226A VAL* 3.9 8.7 - - + +
228A GLU* 2.8 30.0 + - - -
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Residues in contact with LEU 120 (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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90A VAL* 4.0 17.7 - - + -
118A THR* 3.8 19.3 - - + -
119A TRP* 1.3 70.7 - - - +
121A THR* 1.3 59.1 + - - +
133A ASP* 3.3 8.7 - - - +
134A VAL* 2.7 46.0 + - + +
136A ILE* 3.7 17.7 - - + -
203A LEU* 4.2 2.5 - - + -
219A PHE* 3.6 39.7 - - + -
222A LEU* 4.2 16.5 - - + +
223A TYR 3.2 13.9 - - - +
224A PHE* 3.8 23.1 - - + -
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Residues in contact with THR 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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75A PRO* 4.2 25.1 - - + -
119A TRP* 4.3 7.0 - - + +
120A LEU* 1.3 78.1 - - - +
122A ARG* 1.3 62.9 + - - +
123A GLU 2.7 23.3 + - - -
124A LYS 4.4 0.7 + - - -
126A GLN* 3.6 25.4 + - + +
128A GLU 4.6 3.4 - - - +
129A ALA* 5.3 3.4 - - + -
133A ASP* 3.6 9.6 - - + -
222A LEU* 3.4 7.4 - - - -
223A TYR* 2.8 35.0 + - - +
225A THR* 3.3 18.3 - - + +
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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