Contacts of the strand formed by residues 95 - 108 (chain A) in PDB entry 5MJ3
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 GLU 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A HIS* 3.2 4.8 - - - -
92A LYS 2.9 34.5 + - - +
93A GLY 4.1 7.9 - - - +
94A GLY* 1.3 79.6 - - - +
96A VAL* 1.3 71.0 + - - +
97A LEU* 3.3 4.5 - - + +
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Residues in contact with VAL 96 (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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89A THR* 3.7 12.1 - - + -
90A CYS 3.8 3.4 - - - -
91A HIS* 3.6 25.4 - - + +
94A GLY 4.0 2.2 + - - +
95A GLU* 1.3 77.1 + - - +
97A LEU* 1.3 66.7 + - - +
98A SER 3.8 7.9 - - - +
99A HIS* 3.3 35.9 - - + +
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Residues in contact with LEU 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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50A CYS* 3.7 18.4 - - - -
51A ASP 4.2 2.6 - - - +
52A THR* 3.7 34.8 - - + +
54A GLU* 4.3 8.5 - - + -
58A ILE* 4.2 10.3 - - + -
90A CYS 2.9 8.0 + - - +
91A HIS 4.2 3.8 - - - -
92A LYS* 3.4 37.9 - - + +
95A GLU* 3.3 21.8 - - + +
96A VAL* 1.3 77.4 - - - +
98A SER* 1.3 69.1 + - - +
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Residues in contact with SER 98 (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 ASP* 5.9 2.0 - - - -
50A CYS* 4.9 0.2 - - - -
51A ASP* 2.7 47.5 + - - +
60A TRP* 6.4 0.2 - - - -
88A TYR 4.2 0.2 - - - +
89A THR* 3.5 9.0 - - - +
90A CYS* 3.1 39.0 + - - -
96A VAL* 3.8 2.6 - - - +
97A LEU* 1.3 83.1 + - - +
99A HIS* 1.3 71.4 + - - +
100A SER* 5.9 0.2 - - - -
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Residues in contact with HIS 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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29A ASP* 3.5 31.2 + - + +
60A TRP* 6.3 0.2 - - - -
87A GLN* 3.3 31.3 + - + +
88A TYR 3.3 5.4 - - - -
89A THR* 3.1 25.0 + - + +
96A VAL* 3.3 31.7 - - + +
98A SER* 1.3 80.1 - - - +
100A SER* 1.3 67.0 + - - +
101A LEU 4.3 0.7 - - - +
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Residues in contact with SER 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 ASP* 3.6 5.3 + - - -
31A TYR* 3.7 25.5 + - - -
48A LEU* 4.4 24.7 - - - +
49A THR 4.9 8.0 + - - -
60A TRP* 5.2 5.8 - - - -
86A GLY 3.4 2.6 - - - +
87A GLN* 4.3 2.2 - - - -
88A TYR* 2.7 45.5 + - - +
98A SER* 5.9 0.5 - - - -
99A HIS* 1.3 76.2 + - - +
101A LEU* 1.3 58.8 + - - +
102A LEU* 3.8 1.4 + - - -
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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 ASP 3.0 14.5 + - - +
30A VAL* 3.4 10.8 - - + +
31A TYR* 2.8 28.9 + - - +
86A GLY* 3.4 28.3 - - - +
87A GLN* 3.8 17.4 - - + +
99A HIS* 4.3 0.6 - - - +
100A SER* 1.3 71.2 - - - +
102A LEU* 1.3 61.9 + - - +
103A LEU* 4.1 18.4 - - + -
218A LEU* 3.9 14.8 - - + -
407A PG4 3.9 38.6 - - - +
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Residues in contact with LEU 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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23A ILE* 3.8 11.9 - - + -
31A TYR* 3.5 31.2 - - + +
33A VAL* 4.2 13.0 - - + -
46A VAL* 4.7 2.2 - - + -
48A LEU* 4.0 18.4 - - + -
77A ILE* 3.8 28.7 - - + -
79A VAL* 4.1 17.0 - - + -
84A ASP 4.6 1.1 - - - +
85A ALA* 3.4 12.5 - - + +
86A GLY* 2.9 36.7 + - - +
88A TYR* 4.0 17.7 - - + -
100A SER* 4.8 1.6 - - - +
101A LEU* 1.3 74.8 - - - +
103A LEU* 1.3 66.1 + - - +
104A LEU* 5.6 1.3 - - + -
218A LEU* 4.1 1.2 - - - +
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Residues in contact with LEU 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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26A LEU* 4.2 12.3 - - + -
30A VAL* 3.9 24.7 - - + -
31A TYR 2.8 12.6 + - - +
32A VAL* 3.4 4.9 - - + -
33A VAL* 2.8 26.9 + - - +
101A LEU* 4.1 13.7 - - + -
102A LEU* 1.3 80.1 - - - +
104A LEU* 1.3 67.3 + - - +
215A VAL* 3.9 35.9 - - + -
217A LYS 4.1 1.1 - - - +
218A LEU* 3.4 38.1 - - + +
220A TYR* 4.1 14.6 - - + -
407A PG4 4.6 3.8 - - - +
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Residues in contact with LEU 104 (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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33A VAL* 3.5 8.3 - - + +
35A LEU* 3.9 22.7 - - + -
37A TRP* 4.0 9.2 - - + -
79A VAL* 3.4 29.8 - - + -
81A GLU 3.6 32.1 - - - +
82A PHE* 3.7 28.3 - - + +
85A ALA* 3.9 17.0 - - + -
102A LEU* 5.4 1.1 - - + -
103A LEU* 1.3 80.2 - - - +
105A HIS* 1.3 61.2 + - - +
106A LYS* 3.9 4.1 + - + +
218A LEU 3.0 7.7 + - - -
219A LYS* 3.7 5.5 - - - +
220A TYR* 2.9 29.4 + - - +
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Residues in contact with HIS 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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32A VAL* 3.7 18.1 - - + +
33A VAL 3.0 10.5 + - - +
34A GLU* 3.5 4.9 - - - -
35A LEU* 3.0 24.6 + - - -
103A LEU 4.2 0.4 + - - -
104A LEU* 1.3 71.5 - - - +
106A LYS* 1.3 70.2 + - - +
107A LYS 3.6 0.3 + - - -
112A TRP* 3.6 40.3 - + + +
113A SER* 4.8 4.6 + - - -
220A TYR* 3.1 32.4 + + + -
221A GLU* 4.0 10.0 - - - +
222A ASN* 4.3 8.3 + - - -
1D NAG 2.8 48.4 + - - +
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Residues in contact with LYS 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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35A LEU* 3.8 5.2 - - - -
37A TRP* 3.6 55.4 - - + +
82A PHE* 4.3 15.6 - - + -
104A LEU* 3.9 5.5 + - + +
105A HIS* 1.3 75.4 - - - +
107A LYS* 1.3 58.7 + - - +
108A GLU* 3.0 21.4 + - + -
112A TRP* 3.4 8.7 - - - -
113A SER* 3.0 41.1 + - - +
115A ASP* 2.8 29.9 + - - -
219A LYS* 4.0 17.8 - - + +
220A TYR 4.6 0.4 + - - -
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Residues in contact with LYS 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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35A LEU 2.8 16.7 + - - +
36A ASP* 3.6 8.7 - - - +
37A TRP 2.9 26.4 + - - -
105A HIS 3.6 0.4 + - - -
106A LYS* 1.3 71.9 - - - +
108A GLU* 1.3 60.2 + - - +
110A GLY* 3.5 35.7 - - - +
111A ILE 3.4 6.5 - - - +
112A TRP* 3.8 33.9 - - + +
406A PGE 3.1 71.2 + - - +
2D NAG 5.6 2.4 - - - +
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Residues in contact with GLU 108 (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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37A TRP* 3.9 32.0 - - + +
106A LYS* 3.0 29.1 + - + -
107A LYS* 1.3 73.0 - - - +
109A ASP* 1.3 77.6 + - - +
111A ILE* 2.7 28.9 + - - +
113A SER* 3.6 25.6 - - - -
115A ASP* 4.7 4.5 - - - +
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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