Contacts of the helix formed by residues 92 - 105 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B SER* 2.8 19.6 + - - -
90B GLN 3.6 1.6 + - - -
91B THR* 1.3 72.9 - - - +
93B THR* 1.3 63.5 + - - +
94B ALA 3.4 2.0 - - - -
95B GLU* 2.9 27.1 + - - +
96B GLU* 2.9 20.1 + - - +
455B GLN* 3.9 8.9 - - - +
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Residues in contact with THR 93 (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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91B THR* 3.4 6.1 + - - +
92B GLY* 1.3 74.1 - - - +
94B ALA* 1.3 62.4 + - - +
96B GLU* 3.2 7.7 + - - +
97B PHE* 3.1 42.6 + - + -
176B LEU* 3.4 18.6 - - + -
211B ASP* 5.5 0.9 + - - -
215B LEU* 3.7 11.9 - - + -
385B ARG* 4.0 22.2 + - - +
751B FMN 2.9 21.9 + - - -
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TYR* 3.6 2.8 - - - +
88B GLY 3.5 13.9 - - - +
89B SER* 3.7 3.1 - - - -
93B THR* 1.3 74.5 - - - +
95B GLU* 1.3 62.6 + - - +
97B PHE* 3.4 3.5 + - - -
98B ALA* 3.0 24.9 + - - +
139B CYS* 3.4 26.7 - - - +
141B ALA* 4.5 0.4 - - + -
176B LEU* 3.4 24.2 - - + +
751B FMN 2.9 20.6 + - - +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TYR* 3.6 42.7 + - + -
89B SER* 3.7 5.1 + - - +
92B GLY* 2.9 24.7 + - - +
94B ALA* 1.3 79.3 - - - +
96B GLU* 1.3 60.0 + - + +
98B ALA* 3.4 2.1 + - - +
99B ASN* 2.9 39.4 + - - +
360B LYS* 2.7 34.3 + - - -
453B ARG* 6.1 1.8 - - - +
455B GLN* 5.4 1.0 - - - +
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Residues in contact with GLU 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 GLY 2.9 18.0 + - - +
93B THR* 3.7 8.5 - - - +
95B GLU* 1.3 76.7 - - + +
97B PHE* 1.3 64.6 + - + +
99B ASN* 3.2 16.0 + - - +
100B ARG* 2.8 41.0 + - - +
385B ARG* 5.5 11.0 - - - +
387B ASN* 6.2 0.2 - - - +
449B GLU 5.8 0.2 - - - +
450B LEU 4.6 4.4 - - - +
451B LEU 4.3 2.6 - - - +
452B PRO* 3.3 38.6 - - + +
453B ARG 4.6 1.1 + - - -
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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
----------------------------------------------------------
93B THR* 3.1 29.7 + - + -
94B ALA 3.7 5.8 - - - +
96B GLU* 1.3 77.5 - - + +
98B ALA* 1.3 65.3 - - - +
100B ARG* 2.8 21.1 + - - +
101B LEU* 2.8 15.2 + - - +
139B CYS* 4.0 8.5 - - - -
174B PHE* 3.3 36.6 - + - -
176B LEU* 3.8 22.7 - - + -
215B LEU* 4.0 17.3 - - + -
216B GLU* 4.3 18.6 - - - -
219B PHE* 3.7 46.2 - + + -
385B ARG* 4.6 10.3 - - - -
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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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85B VAL* 3.3 31.9 - - + +
87B TYR* 3.8 17.7 - - + -
94B ALA 3.0 15.3 + - - +
95B GLU 3.6 3.4 - - - +
97B PHE* 1.3 78.2 - - - +
99B ASN* 1.3 57.9 + - - +
101B LEU* 3.3 2.8 + - - +
102B SER* 3.0 29.5 + - - -
114B SER* 3.4 16.2 - - - +
139B CYS* 3.7 5.9 - - - -
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Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TYR* 5.3 0.2 - - - -
95B GLU* 2.9 25.6 + - - +
96B GLU* 3.6 16.7 - - - +
98B ALA* 1.3 75.6 - - - +
100B ARG* 1.3 63.9 + - + +
102B SER* 3.3 4.1 + - - -
103B LYS* 3.0 31.5 + - + +
114B SER* 2.7 38.9 + - - -
247B GLN* 5.1 13.3 + - - +
360B LYS* 3.6 24.5 + - - +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLU* 2.8 26.2 + - + +
97B PHE* 2.8 16.8 + - - +
99B ASN* 1.3 72.2 - - + +
101B LEU* 1.3 61.5 + - - +
103B LYS* 3.3 20.4 + - - +
104B ASP* 3.0 29.8 + - - +
216B GLU* 2.9 37.8 + - - -
219B PHE* 3.9 27.2 - - + -
220B ILE* 4.6 7.1 - - - +
223B ARG* 3.5 26.1 - - - +
385B ARG* 4.2 4.8 - - - +
386B THR* 3.7 10.3 + - - -
387B ASN* 3.1 49.8 - - + +
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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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83B ILE* 5.6 1.2 - - - +
85B VAL* 4.3 13.3 - - + +
97B PHE 2.8 6.5 + - - +
98B ALA 3.7 6.1 - - - +
100B ARG* 1.3 76.0 - - - +
102B SER* 1.3 62.1 + - - +
104B ASP* 3.3 30.0 + - - +
105B ALA* 3.4 5.9 + - - +
137B VAL* 4.4 13.9 - - + -
139B CYS* 3.9 28.3 - - - -
219B PHE* 3.6 30.5 - - + -
222B TRP* 4.1 14.1 - - + -
223B ARG* 4.1 10.8 - - + -
226B PHE* 4.1 25.1 - - + -
227B TRP* 3.5 12.6 - - + +
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 5.8 1.1 - - - -
85B VAL* 4.6 6.9 - - - +
98B ALA 3.0 16.8 + - - -
99B ASN* 3.7 7.2 - - - -
100B ARG 3.3 0.2 - - - -
101B LEU* 1.3 75.7 - - - +
103B LYS* 1.3 64.4 + - - +
105B ALA* 3.5 16.5 - - - +
106B HIS 4.6 0.3 + - - -
112B GLY* 3.0 14.5 + - - +
113B MET* 3.0 32.4 + - - -
114B SER* 3.6 16.6 + - - -
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Residues in contact with LYS 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 ASN* 3.0 13.4 + - + +
100B ARG* 3.6 25.2 - - - +
101B LEU 3.3 0.2 - - - -
102B SER* 1.3 75.8 - - - +
104B ASP* 1.3 66.7 + - - +
106B HIS* 3.2 22.7 + - - +
107B ARG* 4.5 1.2 + - - +
245B ILE* 3.9 39.4 + - + +
246B ARG 5.7 0.2 - - - +
247B GLN* 3.8 26.5 - - - +
387B ASN* 4.2 18.8 + - - +
391B GLU* 4.2 22.0 + - - +
449B GLU* 6.1 0.2 - - - +
450B LEU* 5.4 5.3 - - - +
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Residues in contact with ASP 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 ARG 3.0 18.4 + - - +
101B LEU* 3.3 7.7 - - - +
102B SER 3.3 0.2 - - - -
103B LYS* 1.3 74.8 - - - +
105B ALA* 1.3 65.4 + - - +
106B HIS 2.7 5.0 + - - -
107B ARG* 2.9 25.2 + - - +
108B TYR* 3.7 13.5 - - + -
223B ARG* 2.7 50.5 + - - +
227B TRP* 3.1 36.5 + - + +
245B ILE* 5.3 4.8 - - - +
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 3.7 22.2 - - + -
101B LEU 3.4 7.0 + - - +
102B SER* 3.5 9.2 - - - +
104B ASP* 1.3 77.8 - - - +
106B HIS* 1.3 60.5 + - - +
108B TYR* 3.1 12.8 + - - +
110B MET* 2.6 31.9 + - - +
112B GLY* 3.5 25.8 - - - +
227B TRP* 3.7 12.8 - - - -
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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