Contacts of the helix formed by residues 107 - 124 (chain A) in PDB entry 1GXD
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 ASP 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 1.3 71.7 - - - +
108A PRO* 1.3 62.8 - - + +
109A GLU* 3.0 17.1 - - - +
110A THR* 2.4 66.0 + - - -
111A VAL 3.1 8.4 + - - -
191A VAL* 5.6 0.7 - - - +
193A ARG* 3.2 40.2 + - + +
203A TYR* 4.1 3.3 - - - -
304A PRO* 3.6 9.4 - - + +
305A GLU* 4.0 16.5 + - + +
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Residues in contact with PRO 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 3.6 31.9 - - + +
106A LEU 3.4 2.4 - - - +
107A ASP* 1.3 85.2 - - + +
109A GLU* 1.3 61.3 + - + +
110A THR 3.3 0.2 - - - -
111A VAL* 3.8 2.5 - - + -
112A ASP* 3.0 36.0 + - - +
285A TYR* 3.8 29.6 - - + +
304A PRO* 3.2 32.8 - - + +
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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
----------------------------------------------------------
107A ASP* 2.8 12.2 + - - +
108A PRO* 1.3 78.7 - - + +
110A THR* 1.3 67.1 + - - +
112A ASP* 3.4 7.7 + - - +
113A ASP* 3.0 24.8 + - - +
193A ARG* 2.3 40.7 + - - +
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Residues in contact with THR 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 LEU* 3.9 27.1 - - + -
107A ASP* 2.4 42.3 + - - -
109A GLU* 1.3 72.2 - - - +
111A VAL* 1.3 50.7 + - - -
113A ASP* 3.6 4.2 - - + +
114A ALA* 2.7 37.4 + - + +
117A ARG* 5.1 1.5 + - - +
186A LEU* 4.0 22.7 - - + -
193A ARG* 4.9 0.5 - - - -
203A TYR* 2.7 30.5 + - + +
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Residues in contact with VAL 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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102A TYR* 3.5 32.5 - - + -
103A THR* 3.8 29.2 - - + +
106A LEU* 3.8 20.0 - - + +
107A ASP 3.1 7.5 + - - +
108A PRO* 4.0 1.6 - - + +
110A THR* 1.3 73.6 - - - +
112A ASP* 1.3 69.8 + - - +
114A ALA* 3.0 17.2 + - - +
115A PHE* 3.0 44.6 + - + -
144A PHE* 4.9 2.7 - - + -
368A LEU* 3.8 10.3 - - + -
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 5.2 1.6 + - - -
99A ILE* 3.2 15.2 - - - +
102A TYR* 2.5 26.9 + - - -
108A PRO 3.0 25.6 + - - +
109A GLU* 3.6 7.6 - - - +
111A VAL* 1.3 76.7 - - - +
113A ASP* 1.3 63.1 + - - +
115A PHE* 3.6 3.6 + - - +
116A ALA* 3.2 20.7 + - - +
132A ARG* 2.8 34.6 + - - +
285A TYR* 4.5 5.9 + - - -
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Residues in contact with ASP 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 GLU 3.0 17.4 + - - +
110A THR* 3.8 4.5 - - - +
112A ASP* 1.3 73.6 - - - +
114A ALA* 1.3 68.2 + - - +
115A PHE 3.0 0.2 + - - -
116A ALA* 3.0 8.2 + - - +
117A ARG* 2.8 57.7 + - - +
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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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106A LEU* 5.9 0.4 - - + -
110A THR* 2.7 22.9 + - + +
111A VAL* 3.0 9.8 + - - +
113A ASP* 1.3 73.1 + - - +
115A PHE* 1.3 65.2 + - - +
117A ARG* 3.3 23.8 + - - +
118A ALA* 3.2 13.2 + - - +
186A LEU* 4.7 9.0 - - + -
368A LEU* 4.2 26.5 - - + -
369A PHE* 3.8 15.0 - - - +
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Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 5.2 2.7 - - + -
99A ILE* 3.1 35.7 - - + -
111A VAL* 3.0 29.5 + - + -
112A ASP 3.7 4.9 - - - +
114A ALA* 1.3 71.3 - - - +
116A ALA* 1.3 55.9 + - - +
117A ARG 2.6 4.5 + - - -
118A ALA* 2.3 41.3 + - - +
119A PHE* 3.1 7.3 + - + -
142A ILE* 3.1 33.4 - - + -
144A PHE* 4.0 17.0 - + - -
178A PHE* 3.5 28.7 - + - -
368A LEU* 3.9 19.1 - - + -
372A ALA* 3.8 15.0 - - + -
376A PHE* 3.9 14.4 - + + -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 4.0 19.0 + - - +
112A ASP 3.2 11.0 + - - +
113A ASP* 3.0 11.9 + - - +
115A PHE* 1.3 77.9 - - - +
117A ARG* 1.3 61.4 + - + +
119A PHE* 3.7 9.9 + - - +
120A GLN* 3.2 31.8 + - - +
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Residues in contact with ARG 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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110A THR* 5.1 2.0 + - - +
113A ASP* 2.8 46.2 + - - +
114A ALA* 3.4 22.1 - - - +
115A PHE 2.6 4.6 + - - -
116A ALA* 1.3 73.8 - - + +
118A ALA* 1.3 65.5 + - - +
120A GLN* 3.2 22.1 + - - +
121A VAL* 3.3 9.7 + - - +
186A LEU* 4.5 20.2 + - - +
369A PHE* 3.0 59.2 - - + +
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Residues in contact with ALA 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 3.2 3.4 + - - +
115A PHE 2.3 28.4 + - - +
117A ARG* 1.3 66.6 - - - +
119A PHE* 1.3 64.3 + - - +
121A VAL* 2.9 23.7 + - - +
122A TRP* 3.9 7.0 + - - -
369A PHE* 3.8 18.5 - - - +
372A ALA* 3.8 4.9 - - + -
373A ALA* 3.7 22.6 - - - +
376A PHE* 3.4 24.9 - - + -
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Residues in contact with PHE 119 (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 TYR* 3.3 54.1 - + + -
115A PHE* 3.1 9.1 + - + -
116A ALA* 3.9 9.9 - - - +
118A ALA* 1.3 77.2 - - - +
120A GLN* 1.3 54.8 + - + +
122A TRP* 2.7 32.3 + - - +
123A SER* 3.1 10.2 + - - +
130A PHE* 3.5 39.5 - + + -
140A ILE* 3.3 35.9 - - + -
142A ILE* 4.4 0.9 - - + -
376A PHE* 3.6 50.7 - + + -
380A MET* 4.4 1.3 - - + -
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Residues in contact with GLN 120 (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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116A ALA* 3.2 18.6 + - - +
117A ARG* 3.2 19.2 + - - +
118A ALA 3.2 0.4 - - - -
119A PHE* 1.3 80.0 - - - +
121A VAL* 1.3 63.7 + - - +
123A SER* 4.1 10.1 - - - +
124A ASP* 3.0 48.0 + - - +
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Residues in contact with VAL 121 (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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117A ARG 3.3 8.7 + - - +
118A ALA* 2.9 19.3 + - - +
120A GLN* 1.3 78.9 - - - +
122A TRP* 1.3 66.2 + - + +
124A ASP* 4.3 4.3 + - - +
125A VAL* 4.1 10.0 - - - +
369A PHE* 4.0 14.8 - - + -
373A ALA* 4.8 4.0 - - + -
391A LEU* 4.3 5.6 - - + -
402A PHE* 3.4 28.3 - - + -
404A LEU* 3.3 47.8 - - + +
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Residues in contact with TRP 122 (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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118A ALA 3.9 11.9 + - - -
119A PHE* 2.7 16.6 + - - +
121A VAL* 1.3 77.1 - - + +
123A SER* 1.3 63.8 + - - +
124A ASP 3.3 0.2 - - - -
125A VAL* 3.2 5.6 + - - +
126A THR* 2.8 29.5 + - - +
128A LEU* 5.2 1.6 - - + -
130A PHE* 4.4 10.5 - - + -
373A ALA 3.3 12.1 + - - -
376A PHE* 3.7 16.3 - - + +
377A GLY* 3.2 34.2 - - - +
380A MET* 4.6 7.6 - - + -
382A LEU* 4.0 13.9 - - + -
391A LEU* 3.9 16.6 - - + -
392A MET* 4.0 14.8 - - + -
404A LEU* 3.3 38.1 - - + -
408A ASP* 4.1 5.4 - - + -
412A ILE* 3.8 43.1 - - + -
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Residues in contact with SER 123 (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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119A PHE 3.1 5.5 + - - -
120A GLN* 3.1 15.5 + - - -
122A TRP* 1.3 72.2 - - - +
124A ASP* 1.3 57.2 + - - +
125A VAL 2.5 17.9 + - - -
126A THR* 2.6 30.3 + - - +
128A LEU* 3.2 20.1 + - - -
129A ARG* 4.0 20.7 + - - -
130A PHE* 3.6 21.7 + - - -
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Residues in contact with ASP 124 (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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120A GLN* 3.0 37.2 + - - +
121A VAL* 4.5 3.5 - - - +
122A TRP 3.3 0.2 - - - -
123A SER* 1.3 76.1 - - - +
125A VAL* 1.3 65.7 + - + +
129A ARG* 5.2 4.6 + - - +
419A SER* 3.8 11.8 + - - -
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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
------------------------------------------------------------
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