Contacts of the helix formed by residues 92 - 105 (chain A) in PDB entry 3QFR
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 GLY 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A SER* 2.9 16.7 + - - -
90A GLN 3.4 3.6 + - - -
91A THR* 1.3 76.7 - - - +
93A THR* 1.3 59.9 + - - +
94A ALA 3.5 0.2 - - - -
95A GLU* 3.6 16.7 - - - +
96A GLU* 3.2 30.4 + - - +
455A GLN* 4.5 6.7 - - - -
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Residues in contact with THR 93 (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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91A THR* 3.5 6.6 + - - -
92A GLY* 1.3 69.0 - - - -
94A ALA* 1.3 67.0 + - - +
95A GLU 3.0 1.7 + - - -
96A GLU* 3.3 9.4 + - - +
97A PHE* 3.1 37.9 + - + -
176A LEU* 3.7 8.5 - - + -
215A LEU* 3.7 28.3 - - + -
385A ARG* 4.2 20.6 + - - +
751A FMN 2.9 26.5 + - - -
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Residues in contact with ALA 94 (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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87A TYR* 3.6 3.1 - - - +
88A GLY 3.2 28.9 - - - +
89A SER* 3.5 4.7 - - - -
93A THR* 1.3 77.7 - - - +
95A GLU* 1.3 56.7 - - - +
97A PHE* 3.6 4.0 - - - +
98A ALA* 2.9 30.7 + - - +
139A CYS* 3.6 17.2 - - - +
176A LEU* 3.5 22.6 - - + +
751A FMN 2.8 13.4 + - - +
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Residues in contact with GLU 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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87A TYR* 3.9 42.7 + - + -
89A SER* 3.8 3.5 + - - +
92A GLY* 3.6 22.2 + - - +
93A THR 3.0 0.6 - - - -
94A ALA* 1.3 76.6 - - - +
96A GLU* 1.3 56.0 + - + +
98A ALA* 3.1 2.8 + - - +
99A ASN* 2.7 59.2 + - - +
360A LYS* 3.3 34.0 - - - +
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Residues in contact with GLU 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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92A GLY 3.2 18.0 + - - +
93A THR* 3.3 5.7 + - - +
95A GLU* 1.3 79.0 - - + +
97A PHE* 1.3 57.7 + - + +
99A ASN* 3.1 12.8 + - - +
100A ARG* 2.7 50.2 + - + +
385A ARG* 3.2 40.1 + - - +
387A ASN* 5.3 3.6 + - - -
450A LEU 5.3 2.9 - - - +
452A PRO* 3.5 26.6 - - - +
453A ARG 5.1 1.0 + - - -
455A GLN* 6.0 0.3 + - - -
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Residues in contact with PHE 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 THR* 3.1 32.2 + - + +
94A ALA* 3.6 4.9 - - - +
96A GLU* 1.3 78.5 - - + +
98A ALA* 1.3 63.2 + - - +
100A ARG* 3.2 16.4 + - - +
101A LEU* 3.0 25.5 + - - +
139A CYS* 4.2 10.3 - - - -
174A PHE* 3.8 26.5 - + - -
176A LEU* 4.1 11.4 - - + -
215A LEU* 3.8 31.9 - - + -
216A GLU* 3.6 25.1 - - - -
219A PHE* 3.9 39.7 - + + -
385A ARG* 3.9 13.2 - - - -
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Residues in contact with ALA 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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85A VAL* 3.8 27.0 - - + +
87A TYR* 3.8 26.2 - - + -
94A ALA 2.9 18.7 + - - +
95A GLU 3.5 3.6 - - - +
97A PHE* 1.3 76.0 - - - +
99A ASN* 1.3 63.4 + - - +
101A LEU* 3.3 3.3 + - - +
102A SER* 3.1 22.5 + - - -
114A SER* 3.8 4.5 - - - -
139A CYS* 3.8 13.4 - - + -
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Residues in contact with ASN 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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87A TYR* 4.7 1.9 - - - -
95A GLU* 2.7 57.1 + - - +
96A GLU* 3.4 12.1 - - - +
98A ALA* 1.3 73.3 - - - +
100A ARG* 1.3 61.6 - - + +
102A SER* 3.3 3.7 + - - -
103A LYS* 3.2 39.4 + - - +
114A SER* 2.7 32.9 + - - -
247A GLN* 5.3 7.7 + - - +
360A LYS* 4.8 9.9 - - - +
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Residues in contact with ARG 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 GLU* 2.7 33.5 + - - +
97A PHE* 3.2 12.2 + - - +
99A ASN* 1.3 70.1 - - + +
101A LEU* 1.3 66.2 + - - +
103A LYS* 3.6 11.8 + - + +
104A ASP* 3.1 29.7 + - - +
216A GLU* 3.2 22.4 + - - -
219A PHE* 3.4 30.6 - - + -
220A ILE* 3.7 9.3 - - - +
223A ARG* 4.8 11.0 - - - +
385A ARG* 3.8 11.3 - - - +
386A THR* 3.6 21.8 + - - -
387A ASN* 2.9 46.0 - - + +
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Residues in contact with LEU 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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83A ILE* 6.2 0.4 - - - -
85A VAL* 3.8 16.8 - - + -
97A PHE 3.0 15.2 + - - +
98A ALA 3.6 6.7 - - - +
100A ARG* 1.3 75.6 - - - +
102A SER* 1.3 59.7 + - - +
104A ASP* 2.8 28.7 + - - +
105A ALA 3.3 1.7 + - - -
137A VAL* 3.6 31.0 - - + -
139A CYS* 3.8 14.4 - - - -
219A PHE* 4.1 14.1 - - + -
222A TRP* 4.1 17.9 - - + -
223A ARG* 4.0 27.4 - - + -
226A PHE* 4.5 6.5 - - + -
227A TRP* 3.3 21.7 - - + +
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Residues in contact with SER 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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83A ILE* 5.7 1.3 - - - -
85A VAL* 4.2 7.5 - - - +
98A ALA 3.1 10.0 + - - -
99A ASN* 3.5 9.0 - - - -
101A LEU* 1.3 79.4 - - - +
103A LYS* 1.3 61.4 + - - +
104A ASP 3.4 0.2 + - - -
105A ALA* 3.4 19.1 - - - +
106A HIS 4.6 0.2 + - - -
112A GLY* 2.9 32.2 + - - +
113A MET* 3.1 26.0 - - - -
114A SER* 3.5 6.6 + - - -
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Residues in contact with LYS 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 ASN* 3.2 25.2 + - - +
100A ARG* 4.0 10.3 - - + +
101A LEU 3.2 0.2 - - - -
102A SER* 1.3 76.2 - - - +
104A ASP* 1.3 64.6 + - - +
105A ALA 3.3 0.4 + - - -
106A HIS* 3.8 16.2 + - - +
107A ARG* 4.7 3.9 + - - +
245A ILE 5.1 7.0 + - - +
247A GLN* 2.5 58.6 + - - +
449A GLU* 4.8 3.2 + - - +
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Residues in contact with ASP 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 ARG 3.1 18.9 + - - +
101A LEU* 2.8 5.0 + - - +
103A LYS* 1.3 79.6 - - - +
105A ALA* 1.3 64.5 + - - +
107A ARG* 2.9 42.0 + - - +
108A TYR* 3.3 11.8 - - - -
223A ARG* 3.0 34.8 + - - -
227A TRP* 2.9 43.1 + - + +
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Residues in contact with ALA 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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83A ILE* 4.0 17.9 - - + -
101A LEU 3.3 4.0 + - - +
102A SER* 3.4 15.9 - - - +
103A LYS 3.3 0.2 - - - -
104A ASP* 1.3 76.5 - - - +
106A HIS* 1.3 54.3 + - - +
108A TYR* 2.8 27.0 + - - +
110A MET* 3.2 24.6 + - - +
112A GLY* 3.6 23.3 - - - +
227A TRP* 3.8 14.1 - - + -
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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