Contacts of the strand formed by residues 96 - 101 (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 ALA 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ALA* 3.6 15.0 - - + +
27A LEU 4.5 2.9 - - - +
88A LEU* 3.6 35.4 - - + +
93A VAL* 4.0 5.4 - - + -
95A ARG* 1.3 75.9 - - - +
97A HIS* 1.3 68.6 + - - +
98A VAL* 3.4 10.9 + - + +
118A ARG 3.0 6.5 + - - -
119A LEU* 3.5 6.8 - - - -
120A SER* 2.8 22.4 + - - -
121A SER 3.7 0.9 - - - +
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Residues in contact with HIS 97 (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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24A PRO* 4.0 24.1 - - + +
25A ALA 2.9 24.9 + - - +
26A LEU* 3.1 22.6 - - + +
27A LEU 2.8 25.3 + - - -
52A LEU* 4.3 3.2 - - + +
96A ALA* 1.3 69.6 - - - +
98A VAL* 1.3 61.8 + - - +
120A SER* 3.7 18.4 + - - -
121A SER* 2.8 36.3 - - - +
294A THR* 3.4 42.5 + - + -
297A ALA* 4.1 8.4 + - + +
298A ALA* 5.0 7.4 - - + -
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.5 17.3 - - + +
29A VAL* 3.9 15.9 - - + -
88A LEU* 5.0 4.9 - - + -
96A ALA* 3.7 15.3 - - + +
97A HIS* 1.3 77.0 - - - +
99A VAL* 1.3 57.4 + - - +
100A GLY 4.2 0.2 - - - -
108A THR* 3.6 27.8 - - + -
111A ILE* 4.4 11.2 - - + -
119A LEU* 3.3 31.6 - - + -
121A SER* 3.0 7.5 + - - -
122A LEU* 3.5 9.5 - - + +
123A THR* 2.8 33.1 + - - +
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Residues in contact with VAL 99 (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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26A LEU* 3.6 34.5 - - + -
27A LEU 2.9 7.9 + - - -
28A LEU* 3.7 12.7 - - + -
29A VAL* 2.8 30.8 + - - +
39A TRP* 4.1 13.7 - - + -
47A LEU* 5.4 0.2 - - + -
97A HIS* 5.8 0.2 - - + -
98A VAL* 1.3 78.7 - - - +
100A GLY* 1.3 59.4 + - - +
108A THR* 4.3 2.7 - - - -
123A THR* 3.3 22.9 - - + +
125A LEU* 3.8 24.7 - - + -
290A ILE* 4.4 17.5 - - + -
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Residues in contact with GLY 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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29A VAL 3.6 3.8 - - - -
99A VAL* 1.3 72.2 - - - +
101A LEU* 1.3 59.4 + - - -
104A GLY 3.6 6.3 - - - -
105A ALA* 3.6 7.8 - - - +
108A THR* 3.4 25.9 - - - +
123A THR 2.8 13.1 + - - -
124A MET* 3.3 4.7 - - - -
125A LEU* 3.0 28.3 + - - +
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Residues in contact with LEU 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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29A VAL 3.1 7.9 + - - +
30A MET* 3.8 11.4 - - + -
31A GLY* 3.3 11.0 + - - +
39A TRP* 3.6 38.8 - - + -
100A GLY* 1.3 72.9 - - - -
102A SER* 1.3 68.9 + - - +
103A MET 3.3 0.2 + - - -
104A GLY* 2.8 24.4 + - - -
105A ALA 3.6 1.4 - - - +
125A LEU* 3.3 22.4 - - + +
126A LEU* 3.9 21.3 - - + -
278A LEU* 4.0 17.3 - - + -
2712A 1PE 3.2 36.8 - - - -
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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