Contacts of the helix formed by residues 99 - 111 (chain B) in PDB entry 3QVL
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 ILE 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B VAL* 3.8 12.8 - - + -
77B ILE 3.1 12.8 + - - +
78B ALA* 3.6 21.8 - - - +
79B SER* 3.5 19.3 - - - +
80B PHE* 3.5 26.4 - - + +
82B ASP* 3.1 2.2 + - - -
98B GLY* 1.3 70.3 - - - -
100B ALA* 1.3 63.4 + - - +
103B ALA* 3.0 25.6 + - - +
184B SER 4.4 3.6 - - - +
185B GLY* 3.9 21.5 - - - +
204B ASP* 5.6 0.2 - - - +
205B GLY* 3.2 41.2 - - - +
206B VAL* 3.6 15.7 - - + +
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Residues in contact with ALA 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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80B PHE* 3.6 33.7 - - + -
81B GLY 3.9 4.7 - - - +
82B ASP* 3.0 19.8 + - - +
99B ILE* 1.3 76.4 - - - +
101B GLU* 1.3 66.6 + - - +
103B ALA* 4.0 0.3 - - - +
104B MET* 3.0 36.9 + - + +
130B LEU* 3.7 20.9 - - + -
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Residues in contact with GLU 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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82B ASP* 2.9 18.4 + - - +
85B LEU* 4.0 8.1 - - - +
89B ARG* 2.7 37.6 + - - -
97B ILE* 3.6 12.0 - - + +
98B GLY 3.0 23.2 + - - +
100B ALA* 1.3 76.3 - - - +
102B ALA* 1.3 56.2 + - - +
104B MET* 3.8 0.9 - - - +
105B HIS* 2.7 58.3 + - + +
134B TYR* 3.7 25.8 - - + -
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Residues in contact with ALA 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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97B ILE* 3.8 9.2 - - + -
98B GLY 2.9 18.7 + - - +
99B ILE 4.0 0.2 - - - +
101B GLU* 1.3 75.8 - - - +
103B ALA* 1.3 58.0 + - - +
105B HIS* 3.3 6.5 + - - +
106B MET* 3.0 34.1 + - - +
205B GLY 3.9 2.9 - - - +
208B ALA* 3.8 8.1 - - + +
209B ALA* 3.4 37.2 - - + +
212B MET* 4.3 6.7 - - + -
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Residues in contact with ALA 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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80B PHE* 4.7 2.9 - - + -
99B ILE 3.0 18.6 + - - +
100B ALA 4.0 2.5 - - - +
102B ALA* 1.3 76.0 - - - +
104B MET* 1.3 58.1 + - - +
106B MET* 3.5 2.4 + - - +
107B ALA* 3.0 28.9 + - - +
181B VAL* 3.7 28.0 - - + +
182B LEU 5.1 0.2 - - - +
203B ILE* 3.8 20.4 - - + +
205B GLY* 3.7 19.4 - - - +
208B ALA* 4.5 0.2 - - - -
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Residues in contact with MET 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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80B PHE* 4.1 19.1 - - + -
100B ALA* 3.0 23.0 + - + +
101B GLU 3.8 2.5 - - - +
103B ALA* 1.3 72.8 - - - +
105B HIS* 1.3 66.1 + - - +
107B ALA* 3.3 14.2 + - - +
108B THR* 3.3 20.6 + - - +
114B PHE* 3.9 18.9 - - + -
116B ILE* 4.0 15.0 - - + -
127B ALA 4.3 9.2 - - - +
130B LEU* 4.3 10.1 - - + -
131B LEU* 3.8 32.3 - - + -
134B TYR* 3.9 20.9 - - - -
136B PHE* 3.7 20.9 - - + -
181B VAL* 4.5 7.0 - - + -
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Residues in contact with HIS 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 GLU* 2.7 53.1 + - + +
102B ALA* 3.6 8.3 - - - +
104B MET* 1.3 76.3 - - - +
106B MET* 1.3 71.2 + - + +
108B THR* 2.8 23.2 + - - -
109B MET* 3.5 20.7 - - + +
134B TYR* 5.0 6.1 - + + -
136B PHE* 3.5 30.8 - + - -
212B MET* 5.7 3.8 - - + -
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Residues in contact with MET 106 (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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102B ALA 3.0 19.2 + - - +
103B ALA 3.8 4.0 - - - +
105B HIS* 1.3 78.5 - - + +
107B ALA* 1.3 65.4 + - - +
109B MET* 3.0 49.2 + - + +
110B VAL* 3.4 12.5 - - - +
203B ILE* 4.1 16.8 - - + -
208B ALA* 3.7 20.6 - - + -
211B LYS* 6.1 0.7 - - - -
212B MET* 3.5 41.1 - - + -
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Residues in contact with ALA 107 (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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103B ALA 3.0 18.4 + - - +
104B MET 3.6 6.5 - - - +
105B HIS 3.3 0.4 - - - -
106B MET* 1.3 76.8 - - - +
108B THR* 1.3 56.6 + - - +
109B MET 3.3 0.2 + - - -
110B VAL* 3.3 3.4 + - - +
111B ALA* 3.0 32.8 + - - +
113B ARG 5.9 0.2 - - - -
114B PHE* 3.6 30.6 - - + -
179B ALA* 4.9 1.3 - - + -
181B VAL* 3.7 14.8 - - + -
203B ILE* 3.5 15.2 - - + +
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Residues in contact with THR 108 (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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104B MET 3.3 12.7 + - - +
105B HIS* 2.8 21.8 + - - -
107B ALA* 1.3 75.4 - - - +
109B MET* 1.3 62.2 + - - +
110B VAL 3.4 0.4 - - - -
111B ALA 3.5 14.9 + - - +
112B THR 5.6 0.2 - - - -
114B PHE* 4.3 5.8 - - + -
136B PHE* 3.8 30.5 - - + -
139B HIS* 3.8 32.6 - - + +
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Residues in contact with MET 109 (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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105B HIS* 3.5 20.4 - - + +
106B MET* 3.0 46.1 + - + +
108B THR* 1.3 81.8 - - - +
110B VAL* 1.3 63.2 + - + +
212B MET* 5.8 1.6 - - - -
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Residues in contact with VAL 110 (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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106B MET 3.4 17.0 - - - +
107B ALA* 3.6 6.7 - - - +
109B MET* 1.3 87.0 - - + +
111B ALA* 1.3 58.3 + - - +
179B ALA* 4.8 2.0 - - + -
201B PRO* 3.8 37.5 - - + +
203B ILE* 4.1 10.1 - - + -
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Residues in contact with ALA 111 (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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107B ALA 3.0 14.7 + - - +
108B THR* 3.5 16.3 - - - +
109B MET 3.8 0.4 - - - -
110B VAL* 1.3 79.2 - - - +
112B THR* 1.3 65.4 + - - +
113B ARG* 3.7 19.7 - - - +
114B PHE* 5.5 0.2 - - + -
139B HIS* 5.3 0.5 - - - -
178B GLY* 3.9 13.2 - - - +
179B ALA* 3.7 23.8 - - + -
201B PRO* 5.6 0.2 - - + -
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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