Contacts of the helix formed by residues 98 - 118 (chain A) in PDB entry 3GXL
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 THR 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A VAL* 1.3 80.6 - - - +
99A VAL* 1.3 66.9 + - - +
100A GLU* 3.6 8.5 + - - +
101A GLY* 2.9 19.1 + - - -
102A MET* 2.9 21.7 + - - +
215A CYS* 4.0 1.6 - - - -
216A SER 4.5 7.4 - - - +
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Residues in contact with VAL 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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98A THR* 1.3 72.5 - - - +
100A GLU* 1.3 63.4 + - - +
102A MET* 3.2 5.8 + - + +
103A ILE* 3.0 35.7 + - + +
215A CYS* 3.8 20.1 - - - -
216A SER 5.0 4.9 + - - +
261A CYS* 4.5 16.2 - - - -
263A ALA* 3.4 32.5 - - + -
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Residues in contact with GLU 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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98A THR* 3.2 7.9 + - - +
99A VAL* 1.3 81.0 - - - +
101A GLY* 1.3 57.3 + - - +
103A ILE* 3.4 12.3 + - + +
104A LYS* 3.0 49.8 + - + +
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Residues in contact with GLY 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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97A VAL* 4.4 5.2 - - - -
98A THR* 2.9 22.5 + - - -
100A GLU* 1.3 74.8 - - - +
102A MET* 1.3 63.6 + - - +
104A LYS* 3.4 10.9 + - - +
105A LEU* 3.0 33.8 + - - +
145A GLY 4.7 0.6 - - - +
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Residues in contact with MET 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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97A VAL* 3.9 16.2 - - + +
98A THR 2.9 12.8 + - - +
99A VAL* 3.5 10.8 - - + +
101A GLY* 1.3 74.5 - - - +
103A ILE* 1.3 71.1 + - + +
105A LEU* 3.2 3.5 + - - +
106A ALA* 2.9 22.0 + - - +
211A ILE* 3.8 20.8 - - + +
212A ALA* 3.9 11.2 - - - -
215A CYS* 3.8 20.2 - - - -
263A ALA* 4.0 24.0 - - + -
264A LEU* 3.7 30.7 - - + -
267A MET* 3.8 31.6 - - + -
295A LEU* 5.8 0.2 - - + -
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Residues in contact with ILE 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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99A VAL* 3.0 33.8 + - + +
100A GLU* 3.6 11.7 - - + +
102A MET* 1.3 83.5 - - + +
104A LYS* 1.3 58.3 + - + +
106A ALA* 4.0 4.2 - - - +
107A LEU* 2.8 40.2 + - + +
263A ALA* 4.6 0.7 - - + -
267A MET* 5.9 2.5 - - + -
292A LEU* 4.1 13.4 - - + +
295A LEU* 4.1 39.3 - - + +
296A SER* 3.8 32.1 - - - +
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Residues in contact with LYS 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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100A GLU* 3.0 45.9 + - + +
101A GLY* 3.6 8.5 - - - +
102A MET 3.2 0.2 - - - -
103A ILE* 1.3 78.2 - - + +
105A LEU* 1.3 52.7 + - - +
107A LEU* 4.2 4.9 - - - +
108A SER* 2.7 37.3 + - - -
144A ASN 2.9 28.3 + - - -
145A GLY* 3.9 15.4 - - - +
146A THR* 4.4 13.9 - - + +
296A SER* 6.0 1.8 - - - +
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Residues in contact with LEU 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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88A LEU* 4.2 16.2 - - + -
91A TYR* 4.2 12.6 - - + +
92A LEU* 4.4 2.7 - - + -
97A VAL* 4.0 22.2 - - + -
101A GLY 3.0 22.5 + - - +
102A MET 3.2 3.3 + - - +
104A LYS* 1.3 77.9 - - - +
106A ALA* 1.3 58.9 + - - +
108A SER* 3.0 12.8 + - - -
109A THR* 2.9 23.6 + - - -
141A VAL* 4.2 16.2 - - + -
145A GLY 3.5 17.9 - - - +
147A CYS* 3.6 20.7 - - - -
211A ILE* 4.0 30.7 - - + -
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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 MET 2.9 16.4 + - - +
103A ILE* 4.0 2.5 - - - +
105A LEU* 1.3 75.2 - - - +
107A LEU* 1.3 65.9 + - - +
109A THR 3.3 0.7 + - - -
110A ALA* 3.0 19.8 + - - +
208A PHE* 3.4 27.7 - - + -
211A ILE* 4.2 5.3 - - + +
267A MET* 3.6 29.2 - - + -
292A LEU* 3.5 15.7 - - + -
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Residues in contact with LEU 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 ILE* 2.8 23.5 + - + +
104A LYS* 4.2 4.0 - - - +
106A ALA* 1.3 72.4 - - - +
108A SER* 1.3 59.5 + - - +
110A ALA* 3.2 1.4 + - - +
111A SER* 2.7 45.2 + - - +
289A LYS* 3.6 19.3 - - + +
292A LEU* 3.5 24.6 - - + +
293A SER* 3.6 36.3 - - - +
296A SER* 4.2 15.3 - - - +
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Residues in contact with SER 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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58A ASN* 3.2 37.7 - - - +
104A LYS 2.7 23.5 + - - -
105A LEU* 3.0 12.3 + - - -
107A LEU* 1.3 78.1 - - - +
109A THR* 1.3 60.8 + - - +
111A SER* 3.3 1.9 + - - -
112A GLY 3.0 17.8 + - - -
146A THR* 3.8 10.3 - - - -
147A CYS* 2.8 28.0 + - - +
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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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88A LEU* 5.0 3.1 - - - +
105A LEU 2.9 22.7 + - - -
106A ALA 3.7 4.3 - - - -
108A SER* 1.3 75.5 + - - +
110A ALA* 1.3 58.2 + - - +
112A GLY* 3.2 2.1 + - - -
113A LEU* 3.0 27.5 + - - +
134A LEU* 4.8 3.4 - - + -
139A ILE* 3.9 27.9 - - + +
147A CYS* 3.6 21.8 - - - +
149A ILE* 3.8 16.9 - - + +
204A MET* 4.1 21.1 - - + -
207A VAL* 5.1 4.0 - - + -
208A PHE* 4.4 6.1 - - + -
211A ILE* 5.1 1.8 - - - +
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Residues in contact with ALA 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 3.0 17.2 + - - +
107A LEU 3.6 4.0 - - - +
109A THR* 1.3 78.2 - - - +
111A SER* 1.3 57.5 + - - +
113A LEU* 3.8 1.0 - - - +
114A ALA* 2.9 31.6 + - - +
204A MET* 3.7 18.6 - - + -
208A PHE* 4.2 0.4 - - + -
285A ALA* 4.3 4.6 - - - +
288A ILE* 4.0 27.1 - - + -
289A LYS* 4.2 13.9 - - - +
292A LEU* 4.2 5.6 - - + -
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Residues in contact with SER 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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56A HIS* 3.9 9.8 + - - -
58A ASN* 3.4 20.0 - - - -
107A LEU* 2.7 32.9 + - - +
108A SER* 3.6 1.7 - - - -
110A ALA* 1.3 73.6 - - - +
112A GLY* 1.3 62.2 + - - +
114A ALA* 3.5 2.0 + - - +
115A HIS* 3.1 22.9 + - - +
289A LYS* 3.4 39.6 + - - +
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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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56A HIS* 4.4 4.0 - - - -
58A ASN* 3.6 30.7 - - - +
59A ILE* 3.8 3.3 - - - +
108A SER 3.0 11.1 + - - -
109A THR 3.2 3.3 + - - -
111A SER* 1.3 75.8 - - - +
113A LEU* 1.3 59.2 + - - +
115A HIS* 3.4 4.5 + - - +
116A LEU* 3.0 30.3 + - - +
149A ILE* 3.7 8.1 - - - -
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Residues in contact with LEU 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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109A THR 3.0 15.6 + - - +
110A ALA 4.0 2.9 - - - +
112A GLY* 1.3 73.9 - - - +
114A ALA* 1.3 60.5 - - - +
116A LEU* 3.2 18.1 + - + +
117A HIS* 2.8 71.2 + - + +
131A HIS* 4.7 4.3 - - + -
134A LEU* 4.3 11.9 - - + -
149A ILE* 3.6 8.8 - - + +
200A ASP* 4.0 21.1 - - + +
201A ILE* 3.9 16.2 - - + -
204A MET* 3.7 32.5 - - + -
285A ALA* 4.1 2.2 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.8 + - - +
111A SER* 3.8 7.4 - - - +
113A LEU* 1.3 75.6 - - - +
115A HIS* 1.3 58.8 + - - +
117A HIS* 3.4 3.6 + - - +
118A MET* 2.8 34.0 + - - +
285A ALA* 3.6 28.9 - - + +
286A LEU* 4.1 15.0 - - + +
289A LYS* 4.6 10.3 - - + +
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Residues in contact with HIS 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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53A MET* 3.6 17.4 + - + -
54A LEU* 2.7 28.2 + - + -
55A ARG 4.1 3.8 - - - -
56A HIS* 3.3 43.7 - + + +
59A ILE* 3.9 12.3 - - + -
111A SER 3.1 18.1 + - - +
112A GLY 3.5 4.5 - - - +
114A ALA* 1.3 77.2 - - - +
116A LEU* 1.3 62.6 + - - +
118A MET* 3.3 27.7 + - + +
120A ILE* 4.2 8.1 - - + -
126A LYS* 2.9 37.5 + - + -
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Residues in contact with LEU 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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54A LEU* 3.8 27.1 - - + -
59A ILE* 3.6 23.1 - - + -
112A GLY 3.0 16.4 + - - +
113A LEU* 3.5 22.7 - - + +
115A HIS* 1.3 77.4 - - + +
117A HIS* 1.3 55.8 + - + +
126A LYS* 2.9 16.4 + - - +
129A ILE* 2.7 54.4 + - + +
131A HIS* 4.5 14.6 - - + +
149A ILE* 4.4 9.4 - - + -
152A LEU* 4.4 23.8 - - + -
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Residues in contact with HIS 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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113A LEU* 2.8 47.3 + - + +
114A ALA* 3.8 5.4 - - - +
116A LEU* 1.3 74.3 - - - +
118A MET* 1.3 58.5 + - - +
119A GLU 3.6 0.9 + - - -
128A ALA* 3.2 21.1 - - - +
129A ILE 3.2 20.4 - - - +
197A LYS* 3.4 64.7 + - + +
200A ASP* 2.9 27.1 + - + -
201A ILE* 4.1 7.7 - - + +
285A ALA* 3.9 14.2 + - + +
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Residues in contact with MET 118 (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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114A ALA 2.8 18.1 + - - +
115A HIS* 3.4 19.8 - - + +
116A LEU 3.3 0.4 - - - -
117A HIS* 1.3 77.1 - - - +
119A GLU* 1.3 72.6 + - - +
120A ILE* 3.6 33.6 + - + +
126A LYS* 2.8 27.1 + - - -
128A ALA* 4.3 0.7 - - - -
286A LEU* 5.8 8.5 - - - -
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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