Contacts of the strand formed by residues 79 - 92 (chain A) in PDB entry 1REU
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 CYS 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A CYS* 2.0 54.3 - - + -
15A LYS 3.9 0.7 - - - -
43A CYS* 3.8 19.5 - - - +
44A HIS* 3.7 22.2 - - - -
45A GLY 3.4 23.0 + - - +
47A CYS* 3.8 4.6 - - - -
77A ALA 4.0 0.4 + - - -
78A CYS* 1.3 77.1 - - - +
80A VAL* 1.3 65.5 + - - +
111A CYS* 4.2 0.2 - - - -
112A GLY 3.3 5.2 - - - -
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Residues in contact with VAL 80 (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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43A CYS* 3.5 7.2 - - - -
78A CYS* 3.9 20.9 - - + +
79A CYS* 1.3 81.6 - - - +
81A PRO* 1.3 80.3 - - + +
82A THR* 3.5 0.2 - - - +
111A CYS* 3.2 1.4 - - - -
112A GLY 2.8 34.3 + - - +
114A ARG* 3.5 38.1 - - + -
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Residues in contact with PRO 81 (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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42A TYR* 5.7 0.4 - - - -
43A CYS* 3.6 14.4 - - + +
80A VAL* 1.3 94.7 - - + +
82A THR* 1.3 61.9 + - - +
83A GLU 4.8 0.2 - - - +
84A LEU* 3.8 32.9 - - + +
108A VAL* 3.6 26.0 - - + -
110A GLY 3.3 7.9 - - - +
114A ARG* 5.7 0.3 - - - +
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Residues in contact with THR 82 (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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56A ASN* 3.9 17.8 + - - +
80A VAL 3.5 4.7 - - - +
81A PRO* 1.3 74.8 - - - +
83A GLU* 1.3 63.5 + - - +
84A LEU* 4.4 2.0 - - - -
110A GLY* 2.7 21.4 + - - -
111A CYS 3.5 6.1 + - - -
112A GLY* 3.1 35.4 - - - +
114A ARG* 3.9 29.1 + - + +
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Residues in contact with GLU 83 (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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81A PRO 3.5 0.2 - - - -
82A THR* 1.3 83.6 + - - +
84A LEU* 1.3 63.6 + - - +
108A VAL* 3.6 2.3 - - - -
109A GLU* 2.7 46.8 + - + +
110A GLY* 3.2 23.6 + - - +
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Residues in contact with LEU 84 (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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81A PRO* 3.8 31.9 - - + +
82A THR 5.8 1.1 - - - -
83A GLU* 1.3 80.1 - - - +
85A SER* 1.3 60.0 + - - +
104A GLN* 5.5 2.4 + - - -
105A ASP* 3.8 51.4 - - + +
106A MET 4.9 1.1 - - - -
107A VAL 3.1 24.7 - - - +
108A VAL* 3.9 8.7 - - + -
109A GLU* 4.8 1.8 - - - -
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Residues in contact with SER 85 (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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84A LEU* 1.3 75.0 - - - +
86A ALA* 1.3 63.4 + - - +
104A GLN* 5.0 1.6 - - - +
105A ASP 4.4 3.1 - - - -
106A MET 3.0 8.2 + - - -
107A VAL* 2.9 48.3 + - - +
109A GLU* 3.6 22.3 + - - +
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Residues in contact with ALA 86 (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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85A SER* 1.3 80.3 + - - +
87A ILE* 1.3 67.6 + - - +
102A ASN* 4.2 15.7 - - - +
103A TYR 2.7 30.7 - - - +
104A GLN* 3.7 24.1 - - - +
106A MET 4.6 0.7 - - - +
107A VAL* 4.7 0.2 - - - +
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Residues in contact with ILE 87 (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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23A PHE* 4.7 1.3 - - + -
35A PRO* 4.9 5.2 - - + -
38A TYR* 3.9 35.7 - - + -
86A ALA* 1.3 77.0 - - - +
88A SER* 1.3 63.1 + - - +
89A MET* 3.9 30.0 + - + -
102A ASN* 4.7 1.8 - - - -
103A TYR* 3.0 25.5 + - + +
106A MET* 3.9 22.4 - - + +
107A VAL* 3.4 30.5 - - + -
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Residues in contact with SER 88 (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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1A MPD 3.6 25.4 - - - +
35A PRO* 3.8 4.7 - - - +
87A ILE* 1.3 75.6 - - - +
89A MET* 1.3 66.2 + - - +
100A LEU* 4.4 15.9 - - - -
101A LYS 3.6 7.6 - - - -
102A ASN* 2.7 24.5 + - - -
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Residues in contact with MET 89 (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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1A MPD 4.9 1.6 - - - -
23A PHE* 4.0 22.2 - - - -
28A TRP* 6.2 1.1 - - + -
31A TRP* 4.6 3.4 - - + -
32A ILE* 3.9 28.3 - - + -
34A ALA 3.4 8.3 - - - +
35A PRO* 3.8 7.9 - - + -
87A ILE* 3.9 25.1 - - + -
88A SER* 1.3 82.5 - - - +
90A LEU* 1.3 65.4 + - - +
91A TYR* 3.9 4.7 + - + -
99A VAL 3.4 2.6 - - - +
100A LEU* 3.6 5.3 - - - -
101A LYS 3.0 31.8 + - - +
103A TYR* 3.4 46.2 - - + +
106A MET* 4.5 8.5 - - + -
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Residues in contact with LEU 90 (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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1A MPD 3.8 24.5 - - + +
32A ILE* 3.6 1.6 - - - +
33A VAL* 2.9 34.7 + - + -
34A ALA* 2.7 29.8 + - + +
89A MET* 1.3 72.3 - - - +
91A TYR* 1.3 61.6 + - - +
98A VAL* 4.0 20.4 - - + -
99A VAL 3.3 12.8 - - - +
100A LEU* 4.0 22.9 - - + -
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Residues in contact with TYR 91 (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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31A TRP* 3.0 35.0 - + + +
32A ILE* 4.0 8.3 - - + -
33A VAL* 3.9 6.9 - - - +
89A MET* 4.3 5.2 - - + -
90A LEU* 1.3 76.8 - - - +
92A LEU* 1.3 73.1 + - - +
93A ASP* 3.9 23.7 - - + +
97A LYS 3.4 0.7 - - - +
98A VAL* 3.4 2.8 - - - +
99A VAL* 2.7 66.0 + - + +
101A LYS* 3.7 32.7 - - + +
103A TYR* 3.1 31.5 + + - -
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Residues in contact with LEU 92 (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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30A ASP 5.1 9.4 - - - +
31A TRP* 3.0 26.4 + - + +
33A VAL* 4.0 18.2 - - + -
91A TYR* 1.3 86.2 - - - +
93A ASP* 1.3 67.4 - - - +
96A GLU* 3.6 41.5 - - + +
97A LYS 3.6 1.1 - - - -
98A VAL* 3.9 25.4 - - + +
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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