Contacts of the helix formed by residues 101 - 114 (chain A) in PDB entry 1WMA
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 PRO 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A PRO 3.7 7.0 - - - +
100A THR* 1.3 92.4 - - + +
102A PHE* 1.3 66.8 + - - +
103A HIS* 3.3 26.5 - - + +
104A ILE* 3.0 16.0 + - + +
105A GLN 2.9 17.8 + - - -
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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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100A THR 3.4 4.1 + - - -
101A PRO* 1.3 70.5 - - - +
103A HIS* 1.3 59.0 + - - +
105A GLN* 3.1 19.8 + - + +
106A ALA* 2.8 25.3 + - - +
174A PHE* 4.5 2.2 - + - -
178A THR* 3.7 22.7 - - + -
183A HIS* 3.5 31.6 - + - -
190A SER 3.3 21.8 - - - -
192A ALA* 3.8 22.9 - - + -
301A SO4 3.3 24.2 - - - -
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Residues in contact with HIS 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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101A PRO* 3.9 23.6 - - + +
102A PHE* 1.3 81.0 + - - +
104A ILE* 1.3 78.8 + - + +
106A ALA* 3.5 2.3 + - - +
107A GLU* 3.1 29.3 + - - +
175A VAL* 4.6 2.6 - - - +
178A THR* 3.3 29.2 + - - +
179A LYS* 3.6 53.6 + - + +
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Residues in contact with ILE 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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94A PHE* 5.5 0.4 - - + -
100A THR* 3.6 19.5 - - + -
101A PRO* 3.0 18.9 + - + +
103A HIS* 1.3 103.4 - - + +
105A GLN* 1.3 68.0 + - - +
107A GLU* 3.2 16.7 + - - +
108A VAL* 2.8 39.4 + - + +
179A LYS* 5.9 2.2 - - - +
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Residues in contact with GLN 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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94A PHE* 3.3 48.9 - - + +
95A LYS 5.1 2.0 + - - +
98A ASP* 3.5 24.0 + - - +
100A THR* 2.9 26.3 + - + +
101A PRO 2.9 15.8 + - - +
102A PHE* 3.1 23.0 + - + +
104A ILE* 1.3 74.3 - - - +
106A ALA* 1.3 61.0 + - - +
109A THR* 2.8 34.4 + - + +
192A ALA* 4.8 2.9 - - + -
301A SO4 4.4 14.2 + - - -
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Residues in contact with ALA 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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102A PHE* 2.8 13.2 + - + +
103A HIS 3.7 1.1 - - - +
104A ILE 3.2 0.4 - - - -
105A GLN* 1.3 76.8 - - - +
107A GLU* 1.3 62.4 + - - +
109A THR* 3.3 6.4 + - - -
110A MET* 2.9 28.4 + - - +
174A PHE* 3.9 25.8 - - + -
175A VAL* 3.8 5.7 - - + +
178A THR* 3.6 26.9 - - + +
192A ALA* 3.9 11.1 - - + +
196A THR* 4.8 0.5 - - - +
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Residues in contact with GLU 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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103A HIS* 3.1 20.1 + - - +
104A ILE* 3.2 20.8 + - + +
106A ALA* 1.3 75.6 - - - +
108A VAL* 1.3 62.4 + - + +
110A MET* 3.8 1.6 - - - +
111A LYS* 2.8 44.1 + - + +
175A VAL* 3.6 25.9 - - + +
179A LYS* 5.2 8.5 + - - +
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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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92A ILE* 3.6 22.0 - - + +
94A PHE* 4.0 20.4 - - + -
104A ILE* 2.8 39.0 + - + +
107A GLU* 1.3 73.3 - - + +
109A THR* 1.3 64.4 + - - +
111A LYS* 3.3 30.1 + - + +
112A THR* 3.3 11.9 + - - +
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Residues in contact with THR 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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92A ILE* 4.0 21.5 - - + +
93A ALA* 4.6 5.4 - - - -
94A PHE* 3.4 27.6 - - + +
105A GLN* 2.8 26.2 + - + +
106A ALA* 3.3 8.0 + - - -
108A VAL* 1.3 76.9 - - - +
110A MET* 1.3 60.4 + - - +
112A THR* 3.4 0.3 + - - -
113A ASN* 2.9 41.4 + - - +
192A ALA* 4.3 8.0 + - + +
193A TYR* 5.0 9.6 - - + +
196A THR* 3.5 16.9 - - - +
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Residues in contact with MET 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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106A ALA 2.9 19.5 + - - +
107A GLU 3.8 1.6 - - - +
109A THR* 1.3 75.0 + - - +
111A LYS* 1.3 67.1 + - - +
114A PHE* 3.0 28.8 + - - -
115A PHE* 3.0 40.7 + - + -
171A MET* 3.6 46.9 - - - +
174A PHE* 3.8 24.7 - - + -
175A VAL* 3.7 13.7 - - + -
195A VAL* 4.0 5.6 - - + -
196A THR* 3.5 22.0 - - + -
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Residues in contact with LYS 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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64A ASP* 3.3 27.3 - - + +
107A GLU* 2.8 32.1 + - + +
108A VAL* 3.5 22.6 - - + +
109A THR 3.3 0.2 - - - -
110A MET* 1.3 76.7 - - - +
112A THR* 1.3 56.6 + - - +
115A PHE* 3.4 16.1 - - + +
116A GLY 2.8 24.3 + - - -
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Residues in contact with THR 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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37A ARG* 5.7 0.7 + - - -
63A ILE* 3.5 19.4 - - + +
64A ASP* 2.5 27.7 + - - +
91A GLY* 4.3 6.1 - - - -
92A ILE* 3.7 28.4 - - + +
108A VAL* 3.3 4.8 + - - +
110A MET 3.3 0.4 - - - -
111A LYS* 1.3 77.4 - - - +
113A ASN* 1.3 77.9 + - - +
116A GLY* 3.2 15.8 + - - -
117A THR 3.3 8.0 + - - -
309A NDP 3.8 25.6 + - + +
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Residues in contact with ASN 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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90A ALA 5.0 3.8 - - - -
91A GLY* 3.1 10.1 - - - -
92A ILE* 2.9 47.1 + - - +
109A THR* 2.9 22.5 + - - +
112A THR* 1.3 76.3 - - - +
114A PHE* 1.3 57.3 + - - +
117A THR* 2.6 25.6 + - - -
193A TYR* 3.8 15.2 - - - -
196A THR* 3.1 27.8 + - - +
197A LYS* 4.0 10.1 - - - +
200A VAL* 3.2 20.0 - - + +
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Residues in contact with PHE 114 (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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110A MET* 3.0 25.8 + - - +
113A ASN* 1.3 79.5 - - - +
115A PHE* 1.3 99.2 + + - +
116A GLY 3.4 0.2 - - - -
117A THR* 3.4 2.6 + - - -
118A ARG* 2.9 40.8 + - - +
167A LEU* 3.7 28.0 - - + -
168A VAL* 4.0 18.4 - - + -
171A MET* 3.8 16.4 - - + -
196A THR 4.3 5.6 - - - +
199A GLY* 3.6 38.8 - - - -
200A VAL* 4.1 2.9 - - - -
203A LEU* 4.2 14.8 - - + +
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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