Contacts of the helix formed by residues 99 - 111 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A VAL* 3.8 13.5 - - + -
77A ILE 3.1 17.8 + - - +
78A ALA* 3.6 32.1 - - - +
80A PHE* 3.7 27.8 - - + +
82A ASP* 3.1 4.7 + - - +
98A GLY* 1.3 70.1 - - - -
100A ALA* 1.3 63.6 + - - +
102A ALA 4.4 0.2 - - - +
103A ALA* 3.0 25.1 + - - +
182A LEU 6.0 0.2 - - - +
184A SER 4.5 3.1 - - - +
185A GLY* 4.0 20.9 - - - +
205A GLY* 3.2 41.8 - - - +
206A VAL* 3.6 16.4 - - + +
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Residues in contact with ALA 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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80A PHE* 3.2 50.5 - - + +
82A ASP* 3.0 14.9 + - - +
99A ILE* 1.3 77.4 - - - +
101A GLU* 1.3 66.0 + - - +
103A ALA* 3.9 0.5 - - - +
104A MET* 3.0 38.1 + - + +
130A LEU* 3.8 11.0 - - + -
134A TYR* 4.6 0.4 - - + -
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Residues in contact with GLU 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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82A ASP* 3.0 16.9 + - - +
85A LEU* 4.0 8.0 - - - +
89A ARG* 2.7 39.1 + - - -
97A ILE* 3.6 11.0 - - + +
98A GLY 3.0 24.1 + - - +
100A ALA* 1.3 75.6 - - - +
102A ALA* 1.3 56.9 + - - +
104A MET* 3.8 0.9 - - - +
105A HIS* 2.7 58.5 + - + +
134A TYR* 3.7 26.4 - - + +
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Residues in contact with ALA 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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97A ILE* 3.8 8.5 - - + -
98A GLY 3.0 18.3 + - - +
99A ILE 4.0 0.4 - - - +
101A GLU* 1.3 76.4 - - - +
103A ALA* 1.3 57.6 + - - +
105A HIS* 3.4 7.0 + - - +
106A MET* 3.0 34.8 + - - +
205A GLY 3.9 2.7 - - - +
208A ALA* 3.8 7.6 - - + +
209A ALA* 3.5 37.0 - - + +
212A MET* 4.3 6.5 - - + -
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Residues in contact with ALA 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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80A PHE* 4.7 3.6 - - + -
99A ILE 3.0 18.7 + - - +
100A ALA 3.9 2.7 - - - +
102A ALA* 1.3 76.4 - - - +
104A MET* 1.3 57.0 + - - +
106A MET* 3.5 2.6 + - - +
107A ALA* 3.0 28.2 + - - +
181A VAL* 3.7 26.6 - - + +
182A LEU 5.0 0.4 - - - +
203A ILE* 3.9 19.9 - - + +
205A GLY* 3.7 19.7 - - - +
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Residues in contact with MET 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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80A PHE* 4.2 16.4 - - + -
100A ALA* 3.0 27.5 + - + +
101A GLU 3.8 2.0 - - - +
103A ALA* 1.3 72.1 - - - +
105A HIS* 1.3 65.9 + - - +
107A ALA* 3.3 14.4 + - - +
108A THR* 3.3 21.0 + - - +
114A PHE* 3.9 19.0 - - + -
116A ILE* 4.0 15.9 - - + -
127A ALA 4.3 8.1 - - - +
130A LEU* 4.4 5.4 - - + -
131A LEU* 3.8 35.4 - - + +
134A TYR* 3.9 21.8 - - - -
136A PHE* 3.6 22.0 - - + -
181A VAL* 4.5 6.5 - - + -
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Residues in contact with HIS 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLU* 2.7 52.9 + - + +
102A ALA* 3.6 7.6 - - - +
104A MET* 1.3 76.5 - - - +
106A MET* 1.3 70.6 + - + +
108A THR* 2.8 23.1 + - - -
109A MET* 3.5 22.2 - - + +
134A TYR* 5.1 6.1 - + + -
136A PHE* 3.5 31.0 - + - -
212A MET* 5.7 4.5 - - + -
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Residues in contact with MET 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 ALA 3.0 20.7 + - - +
103A ALA 3.8 4.3 - - - +
105A HIS* 1.3 77.7 - - + +
107A ALA* 1.3 64.0 + - - +
109A MET* 3.1 46.6 + - + +
110A VAL* 3.4 14.8 - - + +
203A ILE* 4.1 16.2 - - + -
208A ALA* 3.7 20.2 - - + -
211A LYS* 6.1 0.7 - - - -
212A MET* 3.5 40.8 - - + -
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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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103A ALA 3.0 18.2 + - - +
104A MET 3.3 6.9 + - - +
106A MET* 1.3 77.0 - - - +
108A THR* 1.3 56.4 + - - +
109A MET 3.1 0.2 - - - -
110A VAL* 3.3 3.4 + - - +
111A ALA* 3.1 33.3 + - - +
113A ARG 5.8 0.2 - - - -
114A PHE* 3.6 29.7 - - + -
179A ALA* 5.0 1.6 - - + -
181A VAL* 3.7 14.8 - - + -
203A ILE* 3.5 15.4 - - + +
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Residues in contact with THR 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 MET 3.3 12.8 + - - +
105A HIS* 2.8 21.0 + - - -
107A ALA* 1.3 75.0 - - - +
109A MET* 1.3 62.7 + - - +
110A VAL 3.4 0.7 - - - -
111A ALA 3.5 15.0 - - - +
112A THR 5.6 0.2 - - - -
114A PHE* 4.3 5.8 - - + -
136A PHE* 3.8 26.4 - - + -
139A HIS* 3.7 37.0 - - + +
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Residues in contact with MET 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 HIS* 3.5 22.2 - - + +
106A MET* 3.1 42.7 + - + +
108A THR* 1.3 82.0 - - - +
110A VAL* 1.3 63.5 + - + +
212A MET* 5.8 1.6 - - - -
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Residues in contact with VAL 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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106A MET 3.4 17.3 - - - +
107A ALA* 3.7 6.7 - - - +
109A MET* 1.3 86.4 - - + +
111A ALA* 1.3 58.4 + - - +
179A ALA* 4.8 2.0 - - + -
201A PRO* 3.8 38.8 - - + +
203A ILE* 4.0 11.0 - - + -
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Residues in contact with ALA 111 (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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107A ALA 3.1 19.3 + - - +
108A THR* 3.5 16.9 + - - +
109A MET 3.8 0.4 - - - -
110A VAL* 1.3 82.0 - - - +
112A THR* 1.3 65.8 + - - +
113A ARG 3.7 13.9 - - - +
139A HIS* 5.2 0.2 - - - -
178A GLY* 4.0 13.2 - - - +
179A ALA* 3.7 24.5 - - + -
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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