Contacts of the helix formed by residues 105 - 117 (chain A) in PDB entry 5SWW
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 GLY 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LEU* 5.4 2.9 - - - -
102A PHE 3.1 12.7 + - - -
103A SER 3.5 1.0 - - - -
104A TRP* 1.3 77.2 - - - +
106A CYS* 1.3 58.9 + - - +
107A ALA 3.5 2.0 - - - -
108A GLY* 3.5 5.6 + - - -
109A GLU* 3.0 36.5 + - - +
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Residues in contact with CYS 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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70A HIS* 3.5 18.8 - - - -
72A ALA* 4.1 17.7 - - + -
73A LEU* 3.8 24.9 - - - +
100A PRO* 4.6 3.1 - - + -
101A CYS* 3.8 11.4 + - - +
104A TRP 3.4 3.2 - - - -
105A GLY* 1.3 76.6 - - - +
107A ALA* 1.3 58.6 + - - +
109A GLU* 3.2 5.8 + - - +
110A VAL* 2.9 34.3 + - - +
201A ZN 2.3 36.1 - - - -
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Residues in contact with ALA 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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100A PRO* 4.9 2.4 - - + +
101A CYS 3.1 22.1 + - - +
102A PHE* 4.5 5.1 - - + +
105A GLY 3.5 0.4 - - - -
106A CYS* 1.3 74.2 - - - +
108A GLY* 1.3 57.5 + - - +
110A VAL* 3.4 2.2 + - - +
111A ARG* 2.9 29.3 + - - +
139A ALA* 4.0 31.9 - - + +
142A MET* 4.0 12.6 - - + +
143A LEU* 4.2 20.2 - - + +
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Residues in contact with GLY 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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102A PHE* 5.3 3.2 + - - -
105A GLY* 3.5 8.1 + - - -
106A CYS 3.2 0.4 - - - -
107A ALA* 1.3 80.7 - - - +
109A GLU* 1.3 58.0 + - - +
111A ARG* 3.3 9.8 + - - +
112A ALA* 2.9 27.8 + - - +
142A MET* 3.9 15.7 - - - -
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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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73A LEU* 3.7 28.5 - - + -
76A LEU* 3.8 10.2 - - + +
105A GLY* 3.0 21.3 + - - +
106A CYS 3.7 1.1 - - - +
108A GLY* 1.3 73.7 - - - +
110A VAL* 1.3 60.6 + - - +
112A ALA* 3.2 11.9 + - + +
113A PHE* 2.9 27.4 + - - +
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Residues in contact with VAL 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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72A ALA* 4.3 8.7 - - + -
73A LEU* 6.0 0.2 - - + -
76A LEU* 4.0 20.0 - - + -
94A TRP* 3.9 25.4 - - + -
100A PRO* 5.7 1.6 - - + -
106A CYS 2.9 22.6 + - - +
107A ALA* 3.8 4.3 - - - +
109A GLU* 1.3 74.8 - - - +
111A ARG* 1.3 60.0 + - - +
113A PHE* 3.2 6.1 + - + +
114A LEU* 2.9 36.2 + - + +
122A LEU* 3.8 28.0 - - + -
143A LEU* 3.8 20.2 - - + -
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Residues in contact with ARG 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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107A ALA 2.9 18.0 + - - +
108A GLY* 3.6 8.2 + - - +
110A VAL* 1.3 76.4 - - - +
112A ALA* 1.3 63.3 + - - +
114A LEU* 3.2 3.6 + - - +
115A GLN* 3.0 44.8 + - + +
142A MET* 3.5 49.4 - - + +
143A LEU* 5.1 1.5 - - + +
145A ASP* 5.8 2.9 - - - +
146A ALA* 3.7 31.9 - - + +
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Residues in contact with ALA 112 (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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108A GLY 2.9 15.1 + - - +
109A GLU* 3.2 19.0 + - - +
111A ARG* 1.3 76.5 - - - +
113A PHE* 1.3 61.1 + - - +
115A GLN* 3.2 11.3 + - - +
116A GLU* 3.2 40.0 + - - +
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Residues in contact with PHE 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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75A PHE* 5.6 4.9 - + - -
76A LEU* 4.0 30.3 - - + -
79A VAL* 3.6 39.5 - - + -
84A LEU* 5.1 0.4 - - + -
92A VAL* 6.0 1.1 - - + -
109A GLU 2.9 13.1 + - - +
110A VAL* 3.2 8.5 + - + +
112A ALA* 1.3 75.6 - - - +
114A LEU* 1.3 71.9 + - + +
116A GLU* 3.5 5.6 + - - -
117A ASN* 3.1 57.2 + - + +
120A VAL* 3.9 34.1 - - + -
122A LEU* 6.2 1.6 - - + -
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Residues in contact with LEU 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 VAL* 2.9 32.2 + - + +
111A ARG* 3.2 6.0 + - - +
113A PHE* 1.3 93.3 - - + +
115A GLN* 1.3 60.2 + - + +
117A ASN 3.2 19.0 - - - +
118A THR* 3.9 6.6 + - - +
120A VAL* 4.0 19.1 - - + +
121A ARG* 5.3 0.2 - - - -
122A LEU* 4.0 22.7 - - + +
143A LEU* 5.7 0.9 - - + -
146A ALA* 3.9 30.7 - - + +
147A GLY 5.0 0.4 - - - -
148A ALA* 3.8 30.5 - - + +
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Residues in contact with GLN 115 (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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111A ARG* 3.0 48.0 + - + +
112A ALA* 3.8 8.1 - - - +
113A PHE 3.2 0.2 - - - -
114A LEU* 1.3 78.1 - - + +
116A GLU* 1.3 66.1 + - + +
118A THR* 3.4 18.5 - - - +
146A ALA* 6.0 1.8 - - + +
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Residues in contact with GLU 116 (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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112A ALA* 3.2 28.3 + - - +
113A PHE* 4.2 3.3 - - - +
115A GLN* 1.3 78.8 - - + +
117A ASN* 1.3 71.5 + - - +
118A THR* 3.6 4.7 + - - +
119A HIS* 5.4 0.2 - - - -
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Residues in contact with ASN 117 (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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79A VAL* 6.0 1.0 - - - +
84A LEU* 6.1 1.0 - - - +
113A PHE* 3.1 40.9 + - + +
114A LEU* 3.2 14.1 - - - +
116A GLU* 1.3 88.4 + - - +
118A THR* 1.3 62.7 + - - +
119A HIS* 3.2 35.6 + - + +
120A VAL* 3.5 24.8 + - + +
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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