Contacts of the helix formed by residues 98 - 115 (chain A) in PDB entry 2GFN
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 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 LEU* 1.3 79.2 + - - +
99A GLU* 1.3 54.4 + - - +
100A ARG* 3.4 10.6 + - - +
101A ARG* 3.0 51.4 + - - +
102A LEU* 2.7 38.2 + - - +
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Residues in contact with GLU 99 (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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23A ALA* 3.7 22.6 - - + +
98A ASP* 1.3 72.0 - - - +
100A ARG* 1.3 68.6 + - - +
102A LEU* 4.3 7.9 - - + -
103A ALA* 3.0 26.2 + - - +
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Residues in contact with ARG 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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64A ALA 4.8 1.4 + - - -
67A ILE* 3.7 28.6 - - + +
68A GLN* 2.8 35.5 + - - +
71A ARG* 3.8 23.8 - - - +
93A SER* 3.2 29.1 + - - -
98A ASP* 3.4 12.3 + - - +
99A GLU* 1.3 78.7 - - - +
101A ARG* 1.3 77.5 + - - +
103A ALA* 3.5 4.2 + - - +
104A MSE 3.0 41.6 + - + +
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Residues in contact with ARG 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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92A ALA* 2.7 33.7 + - - +
93A SER* 3.3 31.1 - - - +
94A ILE 4.6 0.2 - - - +
95A LEU 2.9 27.0 + - - +
96A PRO* 3.7 4.7 - - + -
97A LEU* 4.0 25.1 + - - +
98A ASP* 3.0 46.1 + - - +
100A ARG* 1.3 96.5 - - - +
102A LEU* 1.3 61.3 + - - +
104A MSE 3.8 10.3 - - + +
105A THR* 2.8 34.8 + - - -
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Residues in contact with LEU 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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23A ALA* 3.9 14.8 - - + +
96A PRO* 4.0 15.1 - - + +
98A ASP 2.7 24.2 + - - +
99A GLU* 3.8 7.9 - - + +
101A ARG* 1.3 73.0 - - - +
103A ALA* 1.3 62.9 + - - +
105A THR* 3.3 2.4 + - - -
106A ARG* 3.0 75.3 + - - +
174A ILE* 3.8 24.9 - - + -
180A MSE 5.1 5.6 - - + -
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Residues in contact with ALA 103 (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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19A LEU* 3.5 43.4 - - + +
22A ILE* 3.9 13.6 - - + +
23A ALA* 4.0 8.2 - - + +
99A GLU 3.0 18.4 + - - +
100A ARG* 3.8 4.3 - - - +
102A LEU* 1.3 76.0 - - - +
104A MSE 1.3 57.9 + - - +
106A ARG* 3.2 2.1 + - - +
107A VAL* 2.8 34.3 + - - +
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Residues in contact with MSE 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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19A LEU* 4.7 0.6 - - - +
64A ALA* 4.1 16.6 - - + +
68A GLN* 3.7 35.7 - - - +
93A SER 3.3 26.2 - - - +
94A ILE* 4.0 19.5 - - + +
100A ARG* 3.0 25.6 + - + +
101A ARG* 3.8 19.1 - - + +
103A ALA* 1.3 76.1 - - - +
105A THR* 1.3 66.7 + - - +
107A VAL* 3.4 7.1 + - - -
108A PHE* 2.9 48.4 + - + +
128A PHE* 4.0 11.2 - - + -
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Residues in contact with THR 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 ILE 3.8 13.3 + - - -
96A PRO* 3.7 14.3 - - + +
101A ARG 2.8 23.1 + - - -
102A LEU 3.8 3.1 - - - -
104A MSE 1.3 78.7 - - - +
106A ARG* 1.3 57.9 + - - +
108A PHE* 4.1 3.4 - - - +
109A LEU* 2.9 32.9 + - - +
170A ALA* 3.7 28.3 - - + +
171A LEU* 4.0 17.5 - - + +
174A ILE* 3.8 20.0 - - + -
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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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22A ILE* 2.9 44.0 + - + -
23A ALA 3.2 17.6 + - - -
24A ARG 5.1 0.4 - - - -
25A GLU 5.0 0.6 - - - +
26A GLY* 4.1 14.8 - - - +
27A ILE* 3.5 16.0 - - + +
102A LEU* 3.0 49.1 + - + +
105A THR* 1.3 78.3 - - - +
107A VAL* 1.3 61.3 + - - +
109A LEU* 3.8 2.1 - - - +
110A PHE* 3.1 19.1 + - - +
174A ILE* 3.8 25.6 + - + +
116B ALA* 4.5 21.6 + - + +
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Residues in contact with VAL 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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19A LEU* 4.4 2.2 - - + -
22A ILE* 4.0 22.0 - - + -
27A ILE* 3.7 11.4 - - + +
57A LEU* 3.6 26.0 - - + +
60A ALA* 4.2 1.6 - - + +
61A LEU* 3.8 26.7 - - - +
64A ALA* 4.3 6.5 - - + -
103A ALA 2.8 22.7 + - - +
104A MSE 3.5 10.3 - - - +
106A ARG* 1.3 71.2 - - - +
108A PHE* 1.3 75.1 + - + +
110A PHE* 3.4 1.6 + - - +
111A PHE* 3.1 38.6 + - + -
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Residues in contact with PHE 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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61A LEU* 3.5 45.1 - - + -
64A ALA* 4.2 6.3 - - + -
65A GLY* 4.3 4.3 - - - -
104A MSE 2.9 43.1 + - + +
105A THR* 4.1 3.8 - - - +
107A VAL* 1.3 81.7 - - + +
109A LEU* 1.3 50.4 + - - +
111A PHE* 3.2 2.8 + - - +
112A TYR* 2.7 66.4 + + + +
124A GLU* 4.4 9.4 - - - -
125A ILE* 4.5 8.3 - - + -
128A PHE* 3.3 56.5 - + + -
171A LEU* 6.1 1.1 - - + -
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Residues in contact with LEU 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 THR 2.9 18.7 + - - +
106A ARG* 3.8 4.9 - - - +
108A PHE* 1.3 75.5 - - - +
110A PHE* 1.3 62.9 + - - +
112A TYR* 3.1 16.2 + - + +
113A ALA* 3.1 13.7 + - - +
171A LEU* 4.1 29.3 - - + +
174A ILE* 3.8 27.4 - - + -
175A LEU* 4.6 5.4 - - + -
109B LEU* 4.1 24.0 - - + -
112B TYR* 3.7 32.5 - - + +
113B ALA* 3.9 13.0 - - - +
116B ALA* 4.1 5.4 - - + -
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Residues in contact with PHE 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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27A ILE* 3.5 39.9 - - + -
53A ARG* 4.9 11.0 - - - -
54A HIS* 4.8 5.6 - + - -
57A LEU* 3.7 27.6 - - + -
106A ARG 3.1 7.2 + - - +
107A VAL 3.6 4.0 - - - +
109A LEU* 1.3 77.0 - - - +
111A PHE* 1.3 87.9 + + - +
113A ALA* 3.5 4.0 + - - +
114A GLU* 3.1 58.0 + - + +
113B ALA* 4.3 15.6 - - + +
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Residues in contact with PHE 111 (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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54A HIS* 3.5 37.0 - + - -
57A LEU* 3.5 36.6 - - + -
58A LEU* 3.4 31.0 - - + -
61A LEU* 3.5 29.4 - - + -
107A VAL* 3.1 29.8 + - + +
108A PHE 4.0 1.6 - - - +
110A PHE* 1.3 88.7 - + - +
112A TYR* 1.3 66.2 + - - +
114A GLU* 3.9 7.7 - - + +
115A GLY 3.0 18.7 + - - -
121A ALA* 4.5 10.3 - - + +
125A ILE* 3.1 18.4 - - + +
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Residues in contact with TYR 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 PHE* 2.7 49.8 + + + +
109A LEU* 3.1 15.0 + - + +
111A PHE* 1.3 74.1 - - - +
113A ALA* 1.3 63.8 - - - +
115A GLY* 3.3 15.6 + - - -
125A ILE* 3.6 32.5 - - + -
128A PHE* 4.9 6.3 - + - -
129A LEU* 3.7 19.0 - - + +
132A TRP* 4.9 1.7 - - - -
167A ASP* 2.7 33.3 + - - -
171A LEU* 3.8 28.7 - - + -
109B LEU* 3.9 16.9 - - + +
171B LEU* 5.6 6.3 - - + -
172B GLN* 5.5 6.1 - - + -
175B LEU* 3.7 25.9 - - + +
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Residues in contact with ALA 113 (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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109A LEU 3.1 3.3 + - - +
110A PHE 3.9 3.4 - - - +
112A TYR* 1.3 81.5 - - - +
114A GLU* 1.3 62.4 + - + +
115A GLY 3.5 3.6 + - - +
109B LEU* 3.9 25.8 - - + +
110B PHE* 4.3 14.5 - - + +
113B ALA* 3.6 30.7 - - + -
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Residues in contact with GLU 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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54A HIS* 3.7 24.8 + - - +
110A PHE* 3.1 49.3 - - + +
111A PHE* 3.3 15.2 + - + +
112A TYR 3.3 1.0 - - - -
113A ALA* 1.3 77.3 - - + +
115A GLY* 1.3 60.1 + - - +
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Residues in contact with GLY 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 PHE 3.0 14.1 + - - -
112A TYR 3.3 6.0 + - - -
113A ALA 4.3 3.8 - - - -
114A GLU* 1.3 79.3 - - - +
121A ALA 6.2 0.2 - - - -
122A ARG* 4.2 29.6 + - - -
125A ILE* 5.2 1.1 - - - -
175B LEU* 3.3 31.9 - - - -
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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