Contacts of the helix formed by residues 97 - 110 (chain A) in PDB entry 3ISL
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ILE* 3.5 13.6 - - - +
96A TYR* 1.3 81.5 - - - +
98A ARG* 1.3 66.3 + - - +
100A GLY 3.3 9.9 + - - -
101A TYR* 3.6 2.4 - - - -
121A TRP* 3.5 20.3 - - - +
148A GLU* 3.2 20.5 + - - -
150A SER* 3.6 4.9 - - - -
151A THR* 3.8 2.0 - - - -
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Residues in contact with ARG 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 GLY* 1.3 71.9 - - - -
99A PHE* 1.3 105.8 + - + +
101A TYR* 3.2 22.2 + - - +
102A LEU* 3.6 4.2 + - - +
121A TRP* 3.5 22.4 - - + -
149A THR* 4.3 0.2 + - - -
150A SER* 2.8 39.2 + - - +
355A SER* 5.1 2.2 + - - +
356A PHE* 4.4 24.4 + - - +
365A ARG* 3.7 32.1 - - - +
266B ASN* 5.3 9.8 + - - -
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Residues in contact with PHE 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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74A ARG* 4.0 16.4 - - - -
98A ARG* 1.3 120.1 - - + +
100A GLY* 1.3 65.3 + - - +
102A LEU* 3.1 26.9 + - + +
103A LEU* 3.2 16.1 + - - +
145A VAL* 3.6 13.0 - - + +
148A GLU* 3.0 23.1 + - - +
149A THR* 3.3 19.1 - - - -
150A SER* 4.2 2.9 - - - -
174A ASP* 4.2 1.5 - - - +
419A PLP 3.4 68.0 - + + +
266B ASN* 6.0 1.6 - - - -
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Residues in contact with GLY 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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93A ILE* 3.8 1.0 - - - +
94A PRO 5.2 1.1 - - - -
95A ILE* 3.6 27.6 - - - +
96A TYR 5.3 0.2 - - - -
97A GLY 3.3 5.0 + - - -
99A PHE* 1.3 76.5 - - - +
101A TYR* 1.3 59.5 + - - +
103A LEU* 3.3 11.9 + - - +
104A THR* 3.2 24.1 + - - +
145A VAL* 3.5 9.6 - - - +
148A GLU* 2.9 12.9 + - - -
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Residues in contact with TYR 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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95A ILE* 3.5 32.5 - - + +
97A GLY 3.6 9.4 - - - -
98A ARG* 3.2 11.7 + - - +
100A GLY* 1.3 71.9 - - - +
102A LEU* 1.3 66.3 + - - +
104A THR* 3.2 12.1 + - - -
105A GLU* 3.0 27.7 + - + +
116A MET* 4.6 6.3 - - - -
118A GLU* 2.6 37.6 + - - +
121A TRP* 3.8 31.4 + + - -
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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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74A ARG* 3.9 47.3 - - + +
77A ILE* 4.8 8.1 - - + -
98A ARG* 3.6 5.1 + - + +
99A PHE* 3.1 32.1 + - + +
101A TYR* 1.3 73.9 - - - +
103A LEU* 1.3 67.8 + - + +
105A GLU* 3.3 9.0 + - + +
106A ILE* 3.1 36.6 + - + +
174A ASP* 5.5 0.2 - - - +
419A PLP 4.5 6.1 - - + +
249B ASN* 3.4 33.2 - - - +
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Residues in contact with LEU 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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77A ILE* 3.6 32.3 - - + -
81A LEU* 4.3 10.2 - - + +
93A ILE* 3.8 15.6 - - + +
99A PHE 3.2 11.1 + - - +
100A GLY* 3.3 7.4 + - - +
102A LEU* 1.3 78.1 - - + +
104A THR* 1.4 63.5 + - - +
106A ILE* 3.5 5.0 + - - +
107A ALA* 3.0 25.3 + - - +
143A ALA* 3.6 15.2 - - + +
144A MET* 3.5 42.2 - - - +
145A VAL* 4.0 9.2 - - + +
172A ILE* 5.4 2.2 - - + +
174A ASP* 4.5 14.8 - - + +
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Residues in contact with THR 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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93A ILE* 3.5 26.7 - - + -
95A ILE* 3.2 33.9 - - + -
100A GLY 3.2 7.3 + - - +
101A TYR* 3.2 17.2 + - - -
102A LEU 3.2 0.8 - - - -
103A LEU* 1.4 74.1 - - - +
105A GLU* 1.3 62.9 + - - +
107A ALA* 3.4 1.0 + - - +
108A GLU* 2.9 39.8 + - - +
114A VAL* 4.0 15.9 - - + +
116A MET* 4.3 12.0 - - - +
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Residues in contact with GLU 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 TYR* 3.0 18.2 + - + +
102A LEU* 3.4 14.4 - - + +
104A THR* 1.3 77.4 + - - +
106A ILE* 1.3 64.1 + - + +
108A GLU* 3.4 7.3 + - - +
109A ARG* 3.0 68.3 + - - +
249B ASN* 4.0 13.7 - - - +
255B GLN* 6.4 0.4 - - - -
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Residues in contact with ILE 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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74A ARG* 4.3 13.7 - - + +
77A ILE* 4.0 22.0 - - + -
78A GLU* 4.0 20.9 - - + +
81A LEU* 3.7 28.0 - - + -
102A LEU* 3.1 39.2 + - + +
103A LEU* 3.8 4.0 - - - +
105A GLU* 1.3 76.0 - - - +
107A ALA* 1.3 68.6 + - - +
109A ARG* 3.3 5.7 + - - +
110A TYR* 3.1 39.9 + - + -
249B ASN* 4.2 22.2 - - + +
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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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81A LEU* 5.2 3.6 - - + -
85A ILE* 3.9 26.5 - - + -
91A VAL* 4.2 7.0 - - + -
93A ILE* 4.2 9.4 - - + -
103A LEU 3.0 18.2 + - - +
106A ILE* 1.3 77.5 - - - +
108A GLU* 1.3 62.6 + - - +
110A TYR* 3.1 9.4 + - - +
112A ALA* 3.1 27.4 + - + +
114A VAL* 3.8 18.2 - - + -
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Residues in contact with GLU 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 THR* 2.9 24.5 + - - +
105A GLU* 3.8 5.9 - - - +
107A ALA* 1.3 75.8 - - - +
109A ARG* 1.3 57.8 + - + +
111A GLY* 2.8 25.8 + - - -
112A ALA 4.1 12.5 - - - +
114A VAL* 3.8 27.8 + - + +
116A MET* 4.5 12.7 - - - +
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Residues in contact with ARG 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 GLU* 3.0 50.4 + - - +
106A ILE* 3.3 7.2 + - - +
108A GLU* 1.3 77.9 - - + +
110A TYR* 1.3 59.2 + - - +
111A GLY 3.2 2.3 + - - -
245B PRO* 4.1 24.1 - - + +
246B ILE 2.7 39.2 + - - +
247B THR* 3.3 37.2 + - - +
249B ASN* 4.0 16.3 - - - +
252B ASP* 2.8 38.2 + - - +
255B GLN* 3.4 16.9 + - - +
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Residues in contact with TYR 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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78A GLU* 2.8 44.0 + - + +
81A LEU 5.1 0.9 - - - -
82A ALA* 3.7 30.6 - - + +
85A ILE* 3.7 31.6 - - + +
86A GLU 4.2 0.2 - - - -
87A PRO* 3.9 15.3 - - - +
106A ILE* 3.1 37.3 + - + +
107A ALA* 3.1 4.2 + - - +
108A GLU 3.1 0.6 - - - -
109A ARG* 1.3 74.9 - - + +
111A GLY* 1.3 60.3 + - - +
112A ALA 3.4 2.9 + - - -
247A THR* 3.8 31.6 - - + -
248A SER* 3.9 18.7 - - - -
110B TYR* 4.6 0.9 + - - -
247B THR* 3.9 24.7 - - + -
248B SER* 4.0 6.4 + - - -
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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