Contacts of the helix formed by residues 93 - 105 (chain B) in PDB entry 6H7L
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 LEU 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B VAL* 3.2 10.1 + - + +
91B GLY 3.5 0.2 - - - -
92B LEU* 1.3 93.9 - - + +
94B VAL* 1.3 68.5 + - - +
95B VAL 3.5 1.3 - - - -
96B PRO* 3.5 1.5 - - - +
97B PHE* 3.2 45.8 + - + +
117B TRP* 4.1 2.2 + - + -
120B LEU* 3.6 28.9 - - + -
402B 2CV 3.4 44.9 - - + -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL 3.5 8.5 + - - +
90B VAL* 3.2 21.2 + - + +
93B LEU* 1.3 74.6 - - - +
95B VAL* 1.3 64.0 + - - +
98B GLY* 3.1 9.2 + - - -
117B TRP* 2.9 30.5 + - + +
120B LEU* 3.9 22.2 - - + +
121B ASP* 3.6 52.7 - - + +
124B CYS* 4.8 0.9 - - + -
333B TYR* 3.7 23.9 + - + +
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 4.6 6.3 - - + -
52B VAL* 3.5 24.2 - - + -
55B ILE* 4.5 6.7 - - + -
90B VAL* 2.8 40.5 + - + +
91B GLY* 4.6 1.6 - - - -
94B VAL* 1.3 74.6 - - - +
96B PRO* 1.4 55.8 - - + +
98B GLY* 3.1 3.3 + - - +
99B ALA* 2.7 32.8 + - + +
330B TRP* 3.5 30.8 - - + -
333B TYR* 3.7 29.8 - - + -
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Residues in contact with PRO 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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52B VAL* 4.4 12.8 - - + -
91B GLY 3.1 26.7 - - - +
92B LEU* 3.4 14.8 - - - +
93B LEU 3.5 12.8 - - - +
95B VAL* 1.4 88.0 - - + +
97B PHE* 1.3 69.7 + - + +
99B ALA* 3.1 18.5 + - + +
100B THR* 3.2 18.3 + - - +
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Residues in contact with PHE 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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403A 2CV 4.5 22.7 - - - -
92B LEU 5.7 0.4 - - - -
93B LEU* 3.2 37.1 + - + +
96B PRO* 1.3 82.4 - - + +
98B GLY* 1.3 59.9 + - - +
100B THR* 2.7 24.8 + - - -
101B LEU* 3.5 3.6 + - - +
107B TRP* 3.6 33.5 - + + -
109B TRP* 4.4 27.4 - + - -
113B LEU* 4.7 15.5 - - + -
117B TRP* 3.3 30.3 - + + +
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Residues in contact with GLY 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 VAL 3.1 12.7 + - - -
95B VAL* 3.1 5.8 + - - -
97B PHE* 1.3 76.7 - - - +
99B ALA* 1.3 61.2 + - - +
101B LEU* 3.1 12.2 + - - +
102B VAL* 3.4 2.4 + - - +
117B TRP* 3.6 20.5 - - - -
330B TRP* 3.9 3.8 - - - -
333B TYR* 6.0 0.4 - - - -
405B Y00 2.9 33.5 + - - -
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Residues in contact with ALA 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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48B MET* 3.7 25.2 - - + +
52B VAL* 6.0 2.0 - - + -
95B VAL* 2.7 17.2 + - + +
96B PRO* 3.1 13.4 + - + +
98B GLY* 1.3 72.2 - - - +
100B THR* 1.3 61.6 + - + +
102B VAL* 3.5 5.1 + - - +
103B VAL* 3.2 27.7 + - + +
330B TRP* 3.7 16.0 - - + -
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Residues in contact with THR 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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403A 2CV 5.2 11.2 - - - +
96B PRO 3.2 14.1 + - - +
97B PHE* 2.7 22.5 + - - -
99B ALA* 1.3 73.4 - - + +
101B LEU* 1.3 61.8 + - - +
102B VAL 3.1 2.0 - - - -
103B VAL* 3.0 8.0 + - - +
104B ARG* 2.8 44.2 + - + +
106B THR 5.1 0.4 - - - -
109B TRP* 3.1 40.8 - - + -
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Residues in contact with LEU 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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97B PHE 4.0 7.0 - - - +
98B GLY 3.1 10.4 + - - +
100B THR* 1.3 82.4 + - - +
102B VAL* 1.3 57.1 + - - +
105B GLY* 3.2 25.1 + - - -
106B THR* 3.4 37.2 - - - +
107B TRP* 3.6 26.5 - - + +
117B TRP* 4.2 9.0 - - + -
197B GLY 5.0 1.3 - - - +
199B CYS* 4.1 24.9 - - + +
200B ASP* 5.7 2.9 - - - +
405B Y00 3.8 26.5 - - + +
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Residues in contact with VAL 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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44B MET* 3.8 27.9 - - + +
48B MET* 3.5 35.2 - - + -
98B GLY 3.7 4.9 - - - +
99B ALA 3.7 1.8 - - - +
100B THR 3.1 0.6 - - - -
101B LEU* 1.3 78.3 - - - +
103B VAL* 1.3 65.8 + - + +
105B GLY* 3.8 5.0 + - - -
326B VAL* 4.9 6.1 - - + -
330B TRP* 4.0 9.6 - - + +
405B Y00 3.1 23.6 - - - +
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Residues in contact with VAL 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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44B MET* 6.4 0.2 - - - -
45B SER* 4.8 17.7 - - - -
48B MET* 4.9 8.1 - - + -
99B ALA* 3.2 16.6 + - + +
100B THR* 3.0 9.5 + - - +
102B VAL* 1.3 81.2 - - + +
104B ARG* 1.3 78.1 + - + +
51F GLY 4.2 12.5 - - - +
52F LYS* 4.2 28.8 + - + +
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Residues in contact with ARG 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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157A ARG* 5.4 0.4 - - - +
403A 2CV 2.5 36.4 + - - -
100B THR* 2.8 27.8 + - - +
103B VAL* 1.3 85.4 - - + +
105B GLY* 1.3 61.2 + - - +
106B THR* 3.4 21.9 + - + +
108B LEU* 3.7 34.7 - - + +
47F ASP 4.6 4.2 + - - -
48F GLU 3.0 29.2 + - - -
49F TYR* 4.1 2.2 - - - +
50F GLN* 3.0 40.0 + - - +
51F GLY* 3.4 19.8 - - - +
52F LYS* 4.7 11.9 - - - +
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Residues in contact with GLY 105 (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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101B LEU* 3.2 20.9 + - - -
102B VAL 3.8 4.8 + - - -
103B VAL 3.4 2.8 + - - -
104B ARG* 1.3 78.1 - - - +
106B THR* 1.3 61.6 + - - +
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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