Contacts of the helix formed by residues 95 - 109 (chain A) in PDB entry 5WZF
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 SER 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLU* 5.0 6.5 + - - -
86A LEU* 3.8 1.1 - - - +
93A GLU 4.3 0.6 + - - -
94A TYR* 1.3 76.8 - - - +
96A PHE* 1.3 63.4 + - - +
97A VAL* 3.8 6.4 + - - +
98A ASP* 3.2 35.7 + - - +
99A ALA* 3.1 21.5 + - - +
119A ASP* 5.6 0.6 + - - -
45B TRP* 4.2 2.0 - - - +
46B THR* 3.7 27.1 - - - +
50B ARG* 4.5 10.5 - - - -
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Residues in contact with PHE 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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39A HIS* 3.7 28.0 - + - -
79A GLU* 4.1 22.4 - - + -
82A ALA* 4.8 1.8 - - + -
83A TRP* 3.5 47.8 - + - -
86A LEU* 3.9 17.7 - - + -
95A SER* 1.3 69.0 - - - +
97A VAL* 1.3 74.3 + - + +
99A ALA* 3.1 3.1 + - - +
100A THR* 3.0 44.8 + - + +
38B ASN 4.4 7.0 - - - -
39B HIS* 5.6 0.9 - - - -
42B GLY* 3.3 37.7 - - - +
45B TRP* 3.7 8.8 - - + -
46B THR* 3.0 9.3 + - - +
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Residues in contact with VAL 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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5A ASP* 5.2 0.4 - - - +
39A HIS* 4.0 31.4 - - + +
40A VAL* 3.9 24.9 - - + -
43A GLU* 3.4 36.6 - - + +
95A SER* 3.4 6.1 + - - +
96A PHE* 1.3 83.5 - - + +
98A ASP* 1.3 60.8 + - - +
100A THR* 2.6 23.0 + - - -
101A SER* 2.9 18.1 + - - +
46B THR* 4.7 1.7 + - - +
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Residues in contact with ASP 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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5A ASP* 3.6 21.7 - - - +
43A GLU* 5.1 1.9 - - - +
94A TYR* 5.1 1.8 - - + -
95A SER* 3.2 27.9 + - - +
97A VAL* 1.3 80.6 - - - +
99A ALA* 1.3 55.7 + - - +
101A SER* 3.1 5.6 + - - -
102A PHE* 2.8 51.3 + - + -
119A ASP* 3.3 32.1 - - + +
120A PHE* 3.7 12.3 - - - -
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Residues in contact with ALA 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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82A ALA* 3.6 17.8 - - + +
85A TRP* 4.1 9.2 - - + -
86A LEU* 3.5 37.0 - - + -
95A SER 3.1 9.0 + - - +
96A PHE 3.1 9.9 + - - +
98A ASP* 1.3 75.8 - - - +
100A THR* 1.3 57.7 + - - +
102A PHE* 3.4 14.0 + - - +
103A ALA* 3.0 26.2 + - - +
106A ARG* 4.9 1.6 + - - -
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Residues in contact with THR 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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37A SER* 5.0 0.9 + - - -
39A HIS* 4.0 14.1 - - + +
74A VAL* 4.2 19.4 - - + +
79A GLU* 4.4 11.7 - - + -
82A ALA* 3.9 12.8 - - + -
96A PHE* 3.0 45.9 + - + +
97A VAL* 2.6 24.3 + - - -
99A ALA* 1.3 72.0 - - - +
101A SER* 1.3 60.1 + - - +
103A ALA* 3.2 5.3 + - - +
104A VAL* 2.9 35.2 + - - +
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Residues in contact with SER 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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3A PHE* 3.3 34.6 - - - -
5A ASP* 4.6 0.5 + - - -
37A SER* 4.4 1.2 + - - -
40A VAL* 3.4 17.7 - - - +
97A VAL* 2.9 16.7 + - - +
98A ASP* 3.1 9.3 + - - -
100A THR* 1.3 79.2 + - - +
102A PHE* 1.3 61.6 + - - +
104A VAL* 3.2 4.6 + - - +
105A MET* 3.0 29.2 + - - +
120A PHE* 3.8 18.2 - - - -
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Residues in contact with PHE 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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85A TRP* 3.7 23.3 - + + -
94A TYR* 3.7 22.4 - + - -
98A ASP* 2.8 39.5 + - + +
99A ALA* 3.7 4.5 - - - +
101A SER* 1.3 74.6 - - - +
103A ALA* 1.3 57.9 + - - +
105A MET* 3.4 0.6 + - - -
106A ARG* 3.0 49.9 + - - +
119A ASP 3.6 22.7 - - - -
120A PHE* 3.5 41.1 - + - -
123A ALA* 3.4 15.0 - - + -
125A PHE* 3.4 28.2 - + + -
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Residues in contact with ALA 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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78A LEU* 3.8 38.1 - - + +
81A GLN* 4.7 3.8 - - + +
82A ALA* 4.5 3.8 - - + +
99A ALA 3.0 14.3 + - - +
100A THR* 3.6 9.0 - - - +
101A SER 3.2 0.2 - - - -
102A PHE* 1.3 76.6 - - - +
104A VAL* 1.3 62.0 + - - +
106A ARG* 3.4 24.6 + - - +
107A LYS* 3.0 25.1 + - - +
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Residues in contact with VAL 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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3A PHE* 3.9 16.8 - - + -
35A MET* 3.9 26.7 - - - -
37A SER* 4.9 2.0 - - - -
72A GLU* 4.5 16.2 - - + -
74A VAL* 3.9 22.7 - - + -
78A LEU* 3.8 24.7 - - + -
100A THR 2.9 22.0 + - - +
101A SER* 3.6 5.8 - - - +
103A ALA* 1.3 76.2 - - - +
105A MET* 1.3 57.8 + - - +
107A LYS* 3.2 2.8 + - - +
108A LYS* 2.9 34.8 + - + +
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Residues in contact with MET 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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3A PHE* 3.6 27.1 - - + -
101A SER 3.0 18.5 + - - +
102A PHE 3.8 0.7 - - - +
104A VAL* 1.3 76.0 - - - +
106A ARG* 1.3 57.2 + - - +
108A LYS* 3.3 1.5 + - - -
109A GLY* 2.9 9.7 + - - -
110A ILE* 2.9 58.3 + - + +
111A GLN 3.6 17.9 - - - +
112A ASN 3.8 14.1 - - - +
113A ALA* 3.9 8.1 - - + -
120A PHE* 3.7 33.2 - - - -
125A PHE* 3.5 28.0 - - + -
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Residues in contact with ARG 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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81A GLN* 4.6 15.6 + - - +
85A TRP* 3.7 41.5 - - - +
99A ALA 4.9 1.4 + - - -
102A PHE* 3.0 39.2 + - - +
103A ALA* 3.7 28.8 - - - +
105A MET* 1.3 76.2 - - - +
107A LYS* 1.3 63.0 + - - +
109A GLY* 3.3 11.7 + - - -
110A ILE 5.1 0.4 - - - -
123A ALA* 5.9 0.8 + - - +
125A PHE* 4.1 16.1 - - + -
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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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75A THR* 5.7 2.8 + - - +
78A LEU* 4.3 30.6 - - + +
81A GLN* 5.6 5.6 - - - +
103A ALA 3.0 17.7 + - - +
104A VAL* 3.6 5.8 - - - +
106A ARG* 1.3 77.7 - - - +
108A LYS* 1.3 74.4 + - + +
109A GLY 3.5 0.3 + - - -
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Residues in contact with LYS 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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35A MET* 3.8 25.5 - - + +
70A ARG* 5.3 6.5 - - - +
72A GLU* 3.6 38.2 + - - -
104A VAL* 2.9 22.7 + - + +
107A LYS* 1.3 88.8 - - + +
109A GLY* 1.3 63.3 + - - +
110A ILE* 3.8 24.0 - - + +
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Residues in contact with GLY 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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105A MET 2.9 5.8 + - - -
106A ARG* 3.3 7.5 + - - -
107A LYS 3.3 4.4 + - - -
108A LYS* 1.3 79.9 - - - +
110A ILE* 1.3 60.7 + - - +
111A GLN 4.2 0.5 + - - -
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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