Contacts of the helix formed by residues 97 - 110 (chain A) in PDB entry 1EQB
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 SER 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A PRO* 3.1 2.2 - - - +
96A HIS* 1.3 80.3 - - - +
98A GLY* 1.3 61.1 + - - +
99A SER* 3.6 3.6 + - - -
100A GLN* 2.7 33.8 + - - +
101A ALA 3.0 21.3 + - - -
235A ARG 6.0 0.2 - - - -
236A GLY* 3.7 4.5 - - - -
237A GLY* 3.3 21.6 - - - +
1291A PLP 3.5 18.5 + - - -
96B HIS* 3.9 15.2 + - - -
262B GLY 5.1 0.2 + - - -
263B GLY 5.3 1.1 - - - -
265B LEU* 6.1 1.1 - - - -
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Residues in contact with GLY 98 (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 SER* 1.3 74.1 - - - +
99A SER* 1.3 65.8 + - - +
101A ALA* 3.2 5.9 + - - +
102A ASN* 2.9 28.9 + - - +
224A THR* 6.5 0.2 - - - -
225A THR 5.1 2.0 - - - -
226A THR* 3.5 19.9 - - - +
237A GLY* 4.5 1.6 - - - -
1291A PLP 3.3 30.9 + - - -
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Residues in contact with SER 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A SER* 3.3 3.8 - - - -
98A GLY* 1.3 74.4 - - - +
100A GLN* 1.3 59.9 + - - +
102A ASN* 3.3 2.8 + - - +
103A PHE* 2.8 29.8 + - - +
126A HIS* 4.5 1.0 - - - -
128A THR* 3.9 25.7 - - - +
135A PHE* 4.0 4.8 - - - -
1291A PLP 2.8 27.9 + - - -
260B GLY 4.1 6.7 - - - -
261B GLN* 3.5 12.8 - - - -
262B GLY* 3.2 22.4 + - - -
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Residues in contact with GLN 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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95A PRO* 4.4 1.7 - - + +
96A HIS* 4.0 5.4 - - + +
97A SER* 2.7 34.6 + - - +
98A GLY 3.2 0.2 - - - -
99A SER* 1.3 78.8 + - - +
101A ALA* 1.3 65.9 + - - +
103A PHE* 3.3 14.3 + - + +
104A ALA* 3.1 22.5 + - - +
135A PHE* 6.0 0.4 - - - -
260A GLY 5.4 0.2 - - - +
261A GLN* 3.4 29.2 - - + +
96B HIS* 3.5 14.9 - - - -
100B GLN* 3.5 39.8 - - - +
103B PHE* 6.2 1.4 - - - -
260B GLY 3.2 23.9 + - - +
261B GLN* 4.1 4.2 - - - +
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 3.8 24.3 - - + +
97A SER 3.0 17.1 + - - +
98A GLY* 3.6 6.5 - - - +
100A GLN* 1.3 74.3 - - - +
102A ASN* 1.3 64.7 + - - +
104A ALA* 3.2 13.8 + - - +
105A VAL* 3.2 15.8 + - - +
224A THR* 4.0 19.2 - - + +
225A THR 5.0 0.9 - - - +
237A GLY* 4.3 0.9 - - - -
238A LEU 4.0 16.6 - - - +
239A ILE* 4.2 3.9 - - + +
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Residues in contact with ASN 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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98A GLY 2.9 19.8 + - - +
99A SER 3.6 4.3 - - - +
101A ALA* 1.3 72.4 - - - +
103A PHE* 1.3 65.0 + - - +
105A VAL* 3.0 12.9 + - - +
106A TYR* 3.0 31.1 + - + -
128A THR* 2.7 31.6 + - - +
129A HIS* 4.2 3.4 + - - -
135A PHE* 4.8 0.2 - - + -
198A PHE* 3.3 15.7 - - + -
200A ASP* 2.9 21.7 + - - +
224A THR* 2.7 29.5 + - - -
1291A PLP 3.7 5.5 - - - -
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Residues in contact with PHE 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 SER 2.8 20.8 + - - +
100A GLN* 3.3 17.7 + - + +
102A ASN* 1.3 73.6 - - - +
104A ALA* 1.3 64.9 + - - +
106A TYR* 3.3 3.2 + - + +
107A THR* 3.0 54.8 + - + +
135A PHE* 3.5 42.3 - + + -
139A LEU* 4.6 8.7 - - + -
255A ALA 5.5 0.4 - - - -
259A GLY 5.2 0.7 - - - -
260A GLY* 4.3 26.5 - - - -
100B GLN* 6.3 0.9 - - - -
103B PHE* 3.7 38.6 - + - -
135B PHE* 4.5 13.5 - + + -
139B LEU* 5.2 2.7 - - + -
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Residues in contact with ALA 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 GLN 3.1 12.1 + - - +
101A ALA* 3.3 10.8 - - - +
103A PHE* 1.3 80.0 - - + +
105A VAL* 1.3 63.4 + - - +
107A THR* 3.2 9.1 + - - -
108A ALA* 2.9 26.6 + - - +
239A ILE* 4.1 6.7 - - + -
252A LEU* 5.1 1.1 - - + +
255A ALA* 3.4 15.5 - - + +
256A VAL* 3.8 31.4 - - + +
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Residues in contact with VAL 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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101A ALA 3.2 4.0 + - - +
102A ASN 3.0 7.5 + - - +
104A ALA* 1.3 77.1 - - - +
106A TYR* 1.3 61.9 + - - +
109A LEU* 3.2 35.0 + - + +
169A MET* 3.8 21.7 - - + +
198A PHE* 3.8 25.8 - - + -
222A VAL* 3.8 20.9 - - + -
224A THR* 3.5 32.3 - - + -
239A ILE* 4.6 4.5 - - + -
252A LEU* 4.4 13.0 - - + -
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Residues in contact with TYR 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 ASN* 3.0 39.7 + - + -
103A PHE* 3.5 6.1 - - - +
104A ALA 3.2 0.4 - - - -
105A VAL* 1.3 76.7 - - - +
107A THR* 1.3 59.8 - - + +
108A ALA 3.2 0.3 + - - -
110A LEU* 2.8 49.9 + - + +
116A VAL* 4.6 12.3 - - + -
128A THR 2.5 29.8 + - - -
129A HIS* 3.8 2.1 - - - -
135A PHE* 3.8 17.5 - + + -
136A SER* 3.6 12.2 - - - -
140A TYR* 3.5 42.8 - + + +
142A ILE* 5.3 2.4 - - + +
169A MET* 5.0 5.4 - - - -
171A ILE* 3.1 30.6 - - + +
198A PHE* 4.5 9.4 - + - -
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Residues in contact with THR 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 PHE* 3.0 50.4 + - + +
104A ALA* 3.2 10.7 + - - -
106A TYR* 1.3 78.7 - - + +
108A ALA* 1.3 58.8 + - - +
110A LEU 4.0 10.1 - - - +
111A GLU* 5.6 0.3 - - - +
139A LEU* 5.8 2.2 - - + -
140A TYR* 3.9 15.5 - - - +
255A ALA* 4.1 10.6 + - - +
259A GLY 6.0 0.9 - - - -
135B PHE* 5.9 2.5 - - + -
138B LYS* 5.7 8.5 - - - +
139B LEU* 5.9 7.2 - - + -
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Residues in contact with ALA 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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104A ALA 2.9 17.9 + - - +
105A VAL 4.0 3.1 - - - +
106A TYR 3.1 0.2 - - - -
107A THR* 1.3 78.2 - - - +
109A LEU* 1.3 65.0 + - + +
110A LEU 5.1 0.2 - - - -
251A LYS* 3.7 39.8 + - + +
252A LEU* 4.0 18.2 - - + -
255A ALA* 3.4 19.1 - - + -
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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 VAL* 3.2 24.4 + - + +
108A ALA* 1.3 90.6 - - + +
110A LEU* 1.3 66.5 + - - +
168A LYS* 4.0 9.0 + - - -
169A MET* 3.5 30.7 - - + -
196A TYR* 4.0 45.7 - - + +
198A PHE* 5.7 0.7 - - + -
222A VAL* 4.0 18.4 - - + -
248A LEU* 3.4 30.5 - - + -
251A LYS* 5.4 3.4 - - + +
252A LEU* 5.2 1.8 - - + -
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Residues in contact with LEU 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 TYR* 2.8 35.4 + - + +
107A THR* 4.0 12.8 - - - +
109A LEU* 1.3 82.8 - - + +
111A GLU* 1.3 71.5 + - - +
112A PRO* 4.4 1.9 - - - +
114A ASP* 3.4 6.1 - - + +
116A VAL* 3.4 31.9 - - + -
140A TYR* 4.0 16.4 + - + -
168A LYS* 3.4 42.4 - - + +
169A MET* 4.0 32.5 - - + -
196A TYR* 4.9 0.9 - - + -
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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