Contacts of the strand formed by residues 98 - 113 (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 VAL 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL* 5.4 8.3 - - + -
90A LEU* 4.0 25.8 - - + -
91A TYR 3.4 8.5 - - - +
92A LEU* 3.9 16.8 - - + +
96A GLU 3.9 2.1 + - - +
97A LYS* 1.3 73.9 - - - +
99A VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A MET 3.4 1.6 - - - +
90A LEU* 3.3 9.4 - - - +
91A TYR* 2.7 65.0 + - + +
93A ASP* 3.7 22.9 - - + +
97A LYS* 3.1 20.0 - - + +
98A VAL* 1.3 77.5 - - - +
100A LEU* 1.3 69.9 + - - +
101A LYS* 4.2 4.5 - - + -
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Residues in contact with LEU 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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1A MPD 4.8 8.7 - - - +
88A SER* 4.4 17.9 - - - -
89A MET 3.6 15.5 - - - +
90A LEU* 4.0 22.2 - - + -
99A VAL* 1.3 75.8 - - - +
101A LYS* 1.3 60.5 + - - +
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Residues in contact with LYS 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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88A SER* 3.6 2.2 - - - -
89A MET 3.0 30.7 + - - +
91A TYR* 3.7 28.5 - - + +
99A VAL* 3.8 6.0 - - + -
100A LEU* 1.3 78.1 - - - +
102A ASN* 1.3 83.5 + - - +
103A TYR* 3.5 39.2 - - + +
104A GLN 5.2 1.0 - - - +
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Residues in contact with ASN 102 (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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86A ALA* 4.2 19.0 - - - +
87A ILE 4.0 3.0 + - - -
88A SER* 2.7 30.0 + - - -
101A LYS* 1.3 93.0 + - - +
103A TYR* 1.3 61.5 + - - +
104A GLN* 3.9 14.0 + - - +
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Residues in contact with TYR 103 (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* 3.7 19.5 - + - -
86A ALA* 2.7 30.2 - - - +
87A ILE* 3.0 18.0 + - + +
89A MET* 3.4 35.0 - - + -
91A TYR* 3.1 34.8 + + - -
101A LYS* 3.5 48.1 - - + +
102A ASN* 1.3 75.8 - - - +
104A GLN* 1.3 57.5 + - - +
106A MET* 3.3 25.5 - - + +
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Residues in contact with GLN 104 (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 5.5 2.0 + - - -
85A SER* 5.0 1.6 - - - +
86A ALA* 3.7 20.5 - - - +
101A LYS* 5.2 1.4 - - - +
102A ASN* 3.9 15.1 + - - +
103A TYR* 1.3 75.9 - - - +
105A ASP* 1.3 88.0 + - - +
106A MET* 3.4 6.8 + - - +
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Residues in contact with ASP 105 (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* 3.8 48.5 - - + +
85A SER 3.9 5.0 + - - -
104A GLN* 1.3 90.7 + - - +
106A MET* 1.3 62.6 + - - +
107A VAL 3.8 0.4 - - - -
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Residues in contact with MET 106 (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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23A PHE* 4.9 5.8 - - + -
28A TRP* 5.1 10.5 - - + -
38A TYR* 2.8 48.8 + - + +
40A ALA* 3.8 7.1 - - - +
84A LEU* 4.9 2.2 - - - -
85A SER 3.0 6.3 + - - +
87A ILE* 3.9 28.5 - - + -
89A MET* 4.5 15.0 - - + -
103A TYR* 3.3 38.1 - - + +
104A GLN 3.7 6.7 - - - +
105A ASP* 1.3 82.2 - - - +
107A VAL* 1.3 65.1 + - + +
108A VAL* 5.5 1.0 - - - +
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Residues in contact with VAL 107 (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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38A TYR* 3.6 13.5 - - + -
39A HIS 3.4 17.0 - - - +
40A ALA 3.8 2.5 - - - -
41A PHE* 3.9 15.0 - - + -
84A LEU* 3.1 9.0 - - - -
85A SER* 2.9 44.2 + - - +
86A ALA 4.7 0.2 - - - +
87A ILE* 3.4 33.0 - - + -
106A MET* 1.3 80.9 - - - +
108A VAL* 1.3 64.1 + - - +
109A GLU* 3.4 19.5 + - - +
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Residues in contact with VAL 108 (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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16A ARG* 2.7 38.5 + - + -
40A ALA 3.0 17.4 + - - +
41A PHE* 3.9 21.1 - - + +
42A TYR* 4.2 4.7 - - - -
43A CYS* 3.7 25.4 - - - -
81A PRO* 3.6 26.2 - - + -
83A GLU 3.6 3.6 - - - -
84A LEU* 3.9 6.7 - - + -
106A MET 5.5 1.1 - - - +
107A VAL* 1.3 71.2 - - - +
109A GLU* 1.3 56.3 + - - +
110A GLY 3.8 14.8 - - - +
111A CYS* 4.0 4.7 - - - -
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Residues in contact with GLU 109 (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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16A ARG* 3.0 31.5 + - - +
41A PHE* 5.3 0.9 - - - -
83A GLU* 2.7 34.5 + - + +
84A LEU 4.8 0.7 - - - +
85A SER* 3.6 33.9 + - - +
107A VAL* 3.4 13.6 + - - +
108A VAL* 1.3 74.4 - - - +
110A GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 110 (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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16A ARG* 5.4 2.5 - - - -
81A PRO* 3.3 6.4 - - - +
82A THR* 2.7 34.6 + - - -
83A GLU* 3.2 18.1 + - - +
108A VAL* 3.6 5.1 - - - +
109A GLU* 1.3 81.8 - - - +
111A CYS* 1.3 59.0 + - - -
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Residues in contact with CYS 111 (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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14A CYS* 3.9 15.3 - - - -
15A LYS* 3.7 17.5 - - - -
16A ARG* 3.7 19.7 - - - +
43A CYS* 2.0 53.4 - - + -
55A LEU* 4.0 12.0 - - - +
56A ASN* 4.6 5.0 + - - +
79A CYS* 4.2 0.2 - - - -
80A VAL 3.2 5.2 - - - +
82A THR* 3.5 9.2 + - - -
108A VAL* 4.0 1.8 - - - -
110A GLY* 1.3 74.2 - - - -
112A GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 112 (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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14A CYS* 3.9 5.8 - - - -
55A LEU* 4.5 4.5 - - - -
56A ASN* 3.6 13.9 - - - -
78A CYS 3.4 0.3 - - - +
79A CYS* 3.3 3.3 - - - -
80A VAL* 2.8 33.7 + - - +
82A THR* 3.1 16.0 - - - +
111A CYS* 1.3 77.2 - - - +
113A CYS* 1.3 65.4 + - - -
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Residues in contact with CYS 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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14A CYS* 4.2 4.9 - - - -
47A CYS* 2.0 53.8 - - + -
48A PRO* 4.6 0.7 - - - -
55A LEU* 3.9 20.9 - - - -
56A ASN 3.2 7.5 + - - +
57A SER* 3.7 24.4 - - - +
61A ALA* 3.8 6.0 - - + +
77A ALA* 4.1 8.1 - - + -
78A CYS 3.2 3.1 - - - -
112A GLY* 1.3 76.8 - - - -
114A ARG* 1.3 79.7 + - - +
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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