Contacts of the strand formed by residues 119 - 125 (chain A) in PDB entry 1Q0R
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 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LEU* 6.0 0.4 - - + -
95A ARG* 3.6 19.6 + - - -
96A ALA 3.5 1.6 - - - +
98A VAL* 3.3 37.2 - - + -
111A ILE* 3.8 15.5 - - + -
112A ALA* 3.7 34.8 - - + +
115A HIS 4.1 5.6 - - - +
116A HIS* 3.2 18.6 + - + +
117A ASP 3.4 1.2 + - - -
118A ARG* 1.3 80.8 - - - +
120A SER* 1.3 60.3 + - - +
121A SER 4.2 4.7 - - - +
122A LEU* 4.6 10.1 - - + -
238A VAL* 3.4 40.5 - - + +
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Residues in contact with SER 120 (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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95A ARG* 3.4 30.2 + - - +
96A ALA* 2.8 17.6 + - - +
97A HIS* 3.7 24.1 + - - -
119A LEU* 1.3 73.4 - - - +
121A SER* 1.3 62.8 - - - +
238A VAL* 4.1 4.1 - - - +
239A PRO* 3.7 17.0 - - - +
297A ALA* 3.8 13.8 - - - +
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Residues in contact with SER 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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96A ALA 3.7 3.9 + - - +
97A HIS* 2.8 33.6 - - - +
98A VAL* 3.0 24.3 + - - +
119A LEU* 3.5 5.9 - - - +
120A SER* 1.3 80.6 - - - +
122A LEU* 1.3 62.6 + - - +
123A THR* 5.0 1.4 + - - -
238A VAL* 4.2 8.7 - - - -
239A PRO 3.4 13.5 - - - -
293A HIS* 4.0 12.8 + - - -
294A THR* 4.3 4.0 - - - +
297A ALA* 3.8 13.0 - - - -
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Residues in contact with LEU 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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98A VAL* 3.5 22.2 - - + +
108A THR* 3.7 33.9 - - + +
109A GLN* 4.8 1.1 - - - +
111A ILE* 5.9 0.4 - - + -
112A ALA* 3.8 28.0 - - + -
119A LEU* 4.6 9.4 - - + -
121A SER* 1.3 76.0 - - - +
123A THR* 1.3 63.7 + - - +
124A MET* 3.8 30.3 - - + -
236A VAL* 5.6 0.7 - - + -
238A VAL* 4.4 7.8 - - + +
239A PRO 2.9 6.0 + - - +
240A THR* 3.2 19.3 - - + +
241A LEU 2.8 24.6 + - - -
263A ILE* 5.1 4.3 - - + -
293A HIS* 3.1 7.3 - - - -
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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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98A VAL 2.8 13.5 + - - +
99A VAL* 3.3 26.6 - - + +
100A GLY 2.8 25.5 + - - -
121A SER* 5.0 2.4 + - - -
122A LEU* 1.3 71.8 - - - +
124A MET* 1.3 72.2 + - - +
125A LEU* 4.8 0.9 - - + -
241A LEU* 3.2 16.6 - - + +
243A ILE* 4.0 26.2 - - + -
290A ILE* 4.2 13.1 - - + +
293A HIS* 3.4 21.8 + - - -
294A THR* 5.5 1.9 - - - +
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Residues in contact with MET 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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100A GLY 3.3 3.8 - - - -
105A ALA* 3.7 19.3 - - + +
108A THR* 3.3 17.9 - - - +
109A GLN* 3.6 30.5 - - + -
122A LEU* 3.8 19.7 - - + -
123A THR* 1.3 81.8 - - - +
125A LEU* 1.3 61.9 + - - +
240A THR* 3.8 14.4 - - + -
241A LEU 2.9 7.4 + - - +
242A VAL* 3.4 9.1 - - + +
243A ILE* 2.8 26.0 + - - +
259A LEU* 4.0 23.3 - - + -
263A ILE* 3.8 30.3 - - + -
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Residues in contact with LEU 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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39A TRP* 4.7 2.7 - - + -
99A VAL* 3.8 25.1 - - + -
100A GLY 3.0 18.7 + - - +
101A LEU* 3.3 34.1 - - + -
102A SER 2.9 23.6 + - - -
105A ALA* 4.3 0.7 - - - +
123A THR* 4.8 4.5 - - + -
124A MET* 1.3 77.3 - - - +
126A LEU* 1.3 72.3 + - + +
127A GLY* 3.2 5.3 + - - -
242A VAL* 5.8 0.4 - - - -
243A ILE* 3.4 26.7 - - + +
274A MET* 4.4 8.3 - - + -
278A LEU* 4.8 0.9 - - + -
286A LEU* 4.0 31.0 - - + -
290A ILE* 5.7 2.9 - - + -
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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