Contacts of the helix formed by residues 93 - 104 (chain B) in PDB entry 6P1A
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 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLY* 6.0 0.4 - - - -
117A ARG* 4.3 10.1 - - - +
91B GLY 3.7 0.8 + - - -
92B SER* 1.3 75.0 - - - +
94B LYS* 1.3 66.1 + - - +
95B HIS 3.7 0.3 + - - -
96B ALA* 3.1 15.0 + - - +
97B ILE* 3.0 26.7 + - - +
10E T 2.7 57.5 + - - -
11E T 3.8 3.6 - - - -
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Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TYR* 3.7 12.8 - - + -
93B SER* 1.3 71.3 - - - +
95B HIS* 1.3 57.3 + - - +
97B ILE* 3.2 6.9 + - - +
98B ALA* 2.9 31.3 + - - +
127B ARG* 6.1 0.7 - - - -
130B VAL* 4.1 13.7 - - + +
131B ASP* 3.5 35.2 + - - +
134B LEU* 3.6 31.4 - - + -
201B EDO 4.0 27.8 + - - +
11E T 3.3 24.5 + - - +
12E G 3.0 30.8 + - - -
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Residues in contact with HIS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B SER 3.2 0.2 - - - -
94B LYS* 1.3 72.3 - - - +
96B ALA* 1.3 58.0 + - - +
98B ALA* 3.4 5.3 + - - +
99B SER* 2.9 35.6 + - - -
123B LEU* 4.3 19.9 - - + +
127B ARG* 4.2 22.2 - - + +
9E T 5.3 0.7 - - + -
10E T 2.8 54.9 + - + +
11E T 2.7 47.0 + - + +
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B SER* 4.6 7.9 - - - +
93B SER* 3.1 29.7 + - - +
95B HIS* 1.3 77.6 + - - +
97B ILE* 1.3 55.9 + - - +
99B SER* 2.6 22.2 + - - -
100B TYR* 2.9 17.0 + - - +
10E T 3.6 14.1 - - - +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ILE* 3.9 39.3 - - + +
86B SER* 3.9 16.4 - - - -
87B TYR* 4.1 17.0 - - + +
92B SER* 4.1 12.3 - - - -
93B SER 3.0 17.7 + - - +
94B LYS* 3.6 9.2 - - - +
96B ALA* 1.3 76.8 - - - +
98B ALA* 1.3 63.6 + - - +
100B TYR* 3.3 5.1 + - - +
101B TYR* 2.9 53.4 + - + -
130B VAL* 3.9 15.9 - - + -
134B LEU* 5.5 0.4 - - + -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LYS 2.9 16.5 + - - +
95B HIS 3.8 3.6 - - - +
97B ILE* 1.3 76.6 - - - +
99B SER* 1.3 57.8 + - - +
101B TYR* 3.4 2.2 + - - -
102B HIS* 2.8 29.5 + - - +
123B LEU* 3.7 5.1 - - + +
126B CYS* 3.7 10.4 - - + +
127B ARG* 3.6 46.9 - - + +
130B VAL* 4.0 10.3 - - + +
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Residues in contact with SER 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B HIS* 2.9 23.2 + - - -
96B ALA* 2.6 27.4 + - - +
98B ALA* 1.3 75.8 - - - +
100B TYR* 1.3 58.8 + - - +
102B HIS* 3.2 2.3 + - - +
103B ARG* 2.9 42.4 + - - +
123B LEU* 3.8 16.3 - - - +
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Residues in contact with TYR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ALA 2.9 17.3 + - - +
97B ILE* 3.3 5.8 + - - +
99B SER* 1.3 77.7 + - - +
101B TYR* 1.3 88.2 + + - +
103B ARG* 3.5 27.9 + - - +
104B VAL* 3.2 42.5 + - + +
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 2.9 43.0 + - + +
82B GLY* 5.3 2.6 - - - -
83B ILE* 4.1 22.6 + - + +
97B ILE* 2.9 46.3 + - + +
98B ALA* 4.0 5.4 - - - +
100B TYR* 1.3 97.3 - + - +
102B HIS* 1.3 60.9 + - - +
104B VAL* 3.3 15.3 - - + +
105B ALA* 3.1 21.5 - - - +
126B CYS* 4.5 10.0 - - + -
130B VAL* 5.3 3.6 - - + -
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Residues in contact with HIS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA 2.8 18.2 + - - +
99B SER* 3.2 5.6 + - - +
101B TYR* 1.3 75.7 - - - +
103B ARG* 1.3 70.1 + - + +
105B ALA* 3.6 5.6 - - - +
120B LYS* 3.1 38.7 + - + -
121B PRO 2.8 29.6 + - - -
122B SER* 3.6 3.9 - - - -
123B LEU* 3.5 40.2 + - + +
126B CYS* 4.0 9.6 - - - -
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B SER* 2.9 33.1 + - - +
100B TYR* 3.5 36.6 - - - +
102B HIS* 1.3 82.2 - - + +
104B VAL* 1.3 64.0 + - + +
105B ALA 3.5 0.7 + - - -
120B LYS* 3.3 19.1 + - - +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TYR* 3.2 41.6 + - + +
101B TYR* 3.3 15.9 - - + +
103B ARG* 1.3 84.1 - - + +
105B ALA* 1.3 57.0 + - - +
106B ARG* 4.2 1.5 + - + -
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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