Contacts of the strand formed by residues 99 - 107 (chain B) in PDB entry 1REI
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 GLY 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ALA* 3.0 16.3 - - - +
4B MET* 3.7 25.0 - - - +
6B GLN* 3.7 16.2 - - - -
87B TYR* 3.7 4.9 - - - -
88B CYS* 2.8 17.9 + - - -
98B PHE* 1.3 81.0 - - - +
100B GLN* 1.3 61.7 + - - -
101B GLY 3.3 3.2 + - - -
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Residues in contact with GLN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLY 5.0 5.9 - - - +
42A LYS* 5.0 0.9 - - - -
43A ALA* 4.1 13.5 + - - +
4B MET 4.2 3.4 + - - -
5B THR* 3.9 9.5 - - - +
6B GLN* 2.3 49.3 + - - +
9B SER* 3.9 18.6 - - - -
85B THR* 5.4 0.5 - - - +
87B TYR* 3.8 10.4 + - - -
99B GLY* 1.3 71.9 - - - -
101B GLY* 1.3 65.3 + - - +
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLN* 3.4 9.5 + - - -
8B PRO 4.5 0.2 - - - -
9B SER* 3.5 22.3 - - - +
85B THR* 4.2 4.7 - - - -
86B TYR 3.4 12.6 - - - -
87B TYR* 3.6 13.0 - - - -
99B GLY 3.3 4.4 - - - -
100B GLN* 1.3 89.2 - - - +
102B THR* 1.3 64.0 + - - -
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Residues in contact with THR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLN* 3.0 2.2 + - - -
8B PRO* 2.7 29.2 + - + +
9B SER 3.9 1.3 - - - -
11B LEU* 4.0 25.6 - - + -
19B VAL* 6.3 0.2 - - + -
21B ILE* 2.7 45.9 - - + +
84B ALA 3.6 0.5 - - - +
85B THR* 3.2 6.6 - - - -
86B TYR* 3.0 36.0 + - + -
101B GLY* 1.3 70.6 - - - -
103B LYS* 1.3 63.4 + - - +
104B LEU* 3.4 6.6 + - + +
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B SER 3.2 16.8 + - - +
10B SER* 3.3 9.4 + - - +
11B LEU* 3.0 27.9 + - - +
84B ALA 4.0 3.8 - - - +
85B THR* 4.1 16.1 - - + +
101B GLY 4.1 0.8 - - - -
102B THR* 1.3 71.1 - - - +
104B LEU* 1.3 62.0 + - - +
105B GLN* 3.0 33.5 + - + +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.6 21.5 - - + +
19B VAL* 4.1 11.9 - - + -
21B ILE* 6.3 0.4 - - + -
75B ILE* 3.6 20.9 - - + -
78B LEU* 3.5 41.5 - - + -
82B ASP 4.1 6.7 - - - +
83B ILE* 3.4 23.3 - - - +
84B ALA 3.1 19.3 + - - +
86B TYR* 3.9 17.5 - - + -
102B THR* 3.4 4.4 + - + +
103B LYS* 1.3 72.5 - - - +
105B GLN* 1.3 82.3 + - - +
106B ILE* 4.5 4.5 - - + -
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B SER* 3.3 17.4 + - - -
11B LEU 3.0 26.3 + - - +
12B SER* 3.6 12.4 - - - +
13B ALA 3.3 22.1 + - - +
83B ILE* 4.6 7.0 - - + -
103B LYS* 3.0 43.1 + - + +
104B LEU* 1.3 87.9 - - - +
106B ILE* 1.3 66.1 + - - +
107B THR 3.9 0.7 - - - -
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Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA 3.3 8.1 - - - +
15B VAL* 4.4 29.6 - - + +
78B LEU* 3.0 40.2 - - + -
79B GLN 4.3 10.5 - - - +
80B PRO* 4.9 4.5 - - + -
83B ILE* 3.3 37.6 - - + +
104B LEU* 4.5 1.6 - - + -
105B GLN* 1.3 76.7 - - - +
107B THR* 1.3 73.2 + - - +
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Residues in contact with THR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B SER* 2.6 32.8 + - - +
13B ALA* 3.2 17.3 + - - -
14B SER* 3.4 20.7 + - - -
15B VAL* 6.0 0.9 - - - +
105B GLN* 5.1 0.4 - - - +
106B ILE* 1.3 82.2 - - - +
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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