Contacts of the helix formed by residues 94 - 107 (chain A) in PDB entry 4X86
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 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLY* 1.3 76.9 - - - -
95A VAL* 1.3 66.4 + - - +
96A TRP* 3.2 27.8 + - - +
97A GLN* 2.8 34.0 + - - +
98A LEU* 3.2 16.1 + - - +
1098B SER* 3.8 4.3 - - - -
1102B GLN* 5.1 5.8 - - - -
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Residues in contact with VAL 95 (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 SER* 1.3 74.2 - - - +
96A TRP* 1.3 86.3 + - + +
98A LEU* 3.2 3.3 + - + +
99A ILE* 2.8 54.9 + - + +
1095B VAL* 4.3 4.5 - - + +
1098B SER* 3.1 28.8 + - - +
1099B TYR* 3.6 35.2 - - + +
1102B GLN* 4.0 27.2 + - + +
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Residues in contact with TRP 96 (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 SER* 3.1 18.7 - - - +
95A VAL* 1.3 91.2 - - + +
97A GLN* 1.3 58.7 + - + +
99A ILE* 3.9 14.7 - - + +
100A SER* 3.0 29.1 + - - -
116A LEU* 4.1 18.8 - - + +
119A LEU* 3.9 23.6 - - + -
120A GLN* 3.6 49.1 - - + +
123A TYR* 4.0 47.1 - + + -
124A GLU* 5.4 2.7 - - - -
1099B TYR* 5.7 4.9 - + - -
1102B GLN* 4.6 13.4 + - + -
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Residues in contact with GLN 97 (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 GLY* 3.0 15.2 - - - -
94A SER* 2.8 35.6 + - - +
96A TRP* 1.3 78.2 - - + +
98A LEU* 1.3 67.4 + - + +
100A SER* 3.4 6.7 + - - -
101A LYS* 3.2 26.7 + - - +
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Residues in contact with LEU 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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94A SER 3.2 10.7 + - - +
95A VAL* 3.7 5.6 - - - +
97A GLN* 1.3 76.3 - - + +
99A ILE* 1.3 66.3 + - - +
101A LYS* 3.2 24.1 + - + +
102A VAL* 3.3 16.4 + - - +
1094B GLU* 3.8 24.7 - - + +
1095B VAL* 4.4 17.8 - - + +
1098B SER* 3.7 30.3 - - - +
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Residues in contact with ILE 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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95A VAL* 2.8 45.8 + - + +
96A TRP* 3.9 15.0 - - + +
98A LEU* 1.3 72.7 - - - +
100A SER* 1.3 57.7 + - - +
102A VAL* 3.0 9.9 + - - +
103A LEU* 2.8 50.4 + - + +
116A LEU* 4.5 4.7 - - + -
119A LEU* 3.7 32.8 - - + -
1064B LEU* 3.7 30.1 - - + -
1068B VAL* 4.9 6.3 - - + -
1090B LEU* 5.0 3.6 - - + -
1095B VAL* 4.4 4.3 - - + -
1099B TYR* 5.0 1.6 - - + -
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Residues in contact with SER 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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96A TRP 3.0 19.8 + - - -
97A GLN* 3.7 8.1 - - - -
98A LEU 3.2 0.4 - - - -
99A ILE* 1.3 75.6 - - - +
101A LYS* 1.3 63.4 + - - +
103A LEU* 3.4 12.4 + - - +
104A ALA* 3.0 25.1 + - - +
112A ALA* 5.6 1.6 - - - +
116A LEU* 4.4 16.7 - - - +
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Residues in contact with LYS 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 GLN 3.2 15.2 + - - +
98A LEU* 3.2 18.8 + - + +
100A SER* 1.3 77.5 - - - +
102A VAL* 1.3 64.2 + - + +
104A ALA* 3.6 11.9 + - - +
105A ARG* 3.7 17.4 + - - +
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Residues in contact with VAL 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 LEU 3.3 12.9 + - - +
99A ILE* 3.0 8.6 + - - +
101A LYS* 1.3 76.2 - - + +
103A LEU* 1.3 65.6 + - - +
105A ARG* 3.0 18.7 + - - +
106A HIS* 3.1 19.6 - - + -
1086B LEU* 3.9 14.1 - - + -
1089B ASP* 3.7 41.7 - - + +
1090B LEU* 3.7 26.7 - - + -
1095B VAL* 4.3 14.6 - - + -
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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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99A ILE* 2.8 38.6 + - + +
100A SER* 3.4 9.2 + - - +
102A VAL* 1.3 76.8 - - + +
104A ALA* 1.3 57.2 + - - +
105A ARG 3.1 0.2 - - - -
106A HIS* 3.2 2.2 + - - +
107A PHE* 3.0 61.3 + - + +
112A ALA* 3.7 33.0 - - + +
115A VAL* 4.1 9.2 - - + -
116A LEU* 4.0 20.9 - - + +
119A LEU* 5.8 0.7 - - + -
1068B VAL* 4.1 20.2 - - + -
1086B LEU* 4.4 7.6 - - + -
1090B LEU* 5.4 0.9 - - + -
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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 SER* 3.0 17.5 + - - +
101A LYS* 3.9 9.0 - - - +
102A VAL 3.1 0.6 - - - -
103A LEU* 1.3 75.4 - - - +
105A ARG* 1.3 60.2 + - + +
106A HIS 3.4 0.4 - - - -
107A PHE 4.2 10.8 - - - +
112A ALA* 4.7 6.5 - - + +
1080B LEU* 5.8 0.9 - - - +
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Residues in contact with ARG 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 LYS 3.7 15.9 - - - +
102A VAL* 3.0 13.9 + - - +
104A ALA* 1.3 81.1 - - + +
106A HIS* 1.3 72.7 + - + +
107A PHE 3.9 0.2 - - - -
1080B LEU* 5.2 5.6 - - - +
1081B THR* 3.9 10.4 - - - +
1089B ASP* 3.0 29.6 + - - -
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Residues in contact with HIS 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 VAL* 3.1 25.6 - - + +
103A LEU 3.2 1.4 + - - -
105A ARG* 1.3 92.8 + - + +
107A PHE* 1.3 63.2 + - + +
1079B PRO* 3.1 10.2 - - + +
1080B LEU* 2.6 34.3 + - - -
1081B THR* 2.7 34.0 + - + +
1085B SER* 3.6 27.6 + - - -
1086B LEU* 3.8 32.8 + - + -
1089B ASP* 2.7 31.3 + - - +
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Residues in contact with PHE 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 LEU* 3.0 44.2 + - + +
104A ALA* 4.2 10.9 - - - +
106A HIS* 1.3 83.0 - - + +
108A SER* 1.3 72.2 + - - +
109A ALA* 3.8 0.3 + - - -
111A ASP* 4.0 3.8 - - + -
112A ALA* 3.8 13.0 - - - +
115A VAL* 4.4 8.5 - - + -
1068B VAL* 5.0 0.4 - - + -
1072B ALA* 4.1 11.0 - - + -
1077B ALA* 3.7 33.2 - - + -
1078B ARG 3.7 13.9 - - - -
1079B PRO* 3.7 20.9 - - + -
1080B LEU* 3.7 13.3 - - - +
1086B LEU* 3.7 28.5 - - + -
1202B SO4 3.8 15.5 - - - -
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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