Contacts of the strand formed by residues 75 - 86 (chain B) in PDB entry 3QNF
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 THR 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B ALA* 3.5 0.7 - - - +
70B ASN* 2.6 39.6 + - + +
73B THR* 3.3 17.9 + - - +
74B LEU* 1.3 75.6 + - - +
76B PHE* 1.3 70.0 + - - +
77B TRP* 4.7 1.8 - - + +
152B ALA* 5.9 3.1 - - + -
153B GLY 3.7 9.3 + - - +
154B ASN* 3.1 21.3 + - - -
155B LEU* 4.4 3.3 - - - +
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Residues in contact with PHE 76 (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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67B ILE* 4.1 12.3 - - + -
68B HIS 3.1 11.9 - - - +
69B ALA* 3.5 17.7 - - + -
75B THR* 1.3 81.2 - - - +
77B TRP* 1.3 66.1 + - - +
100B LEU* 4.1 11.7 - - + -
151B TYR* 3.9 10.3 - + - -
152B ALA* 3.6 3.2 - - - +
153B GLY* 2.8 59.3 + - - +
154B ASN 3.7 12.8 - - - -
155B LEU* 3.8 18.2 - - + -
162B PHE* 3.8 26.9 - + + -
189B MET 3.6 22.9 - - - -
190B ALA* 3.3 22.9 - - - -
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Residues in contact with TRP 77 (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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66B LEU* 3.7 26.7 - - + -
67B ILE* 3.7 3.3 - - - +
68B HIS* 2.6 65.8 + - + +
75B THR* 4.7 2.1 - - + +
76B PHE* 1.3 77.4 - - - +
78B GLY* 1.3 66.7 + - - +
79B THR* 3.1 22.5 + - - -
150B HIS* 4.4 12.3 + + - +
151B TYR 3.3 27.3 - - - +
152B ALA* 4.4 6.7 - - + +
208B ARG* 3.3 28.5 - - - -
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Residues in contact with GLY 78 (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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66B LEU 3.2 11.2 - - - -
67B ILE* 4.2 1.1 - - - -
77B TRP* 1.3 86.7 + - - +
79B THR* 1.3 61.5 + - - -
151B TYR* 2.8 62.3 + - - +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASP 3.6 2.8 - - - +
66B LEU* 2.9 45.0 + - - +
67B ILE* 5.8 0.2 - - - +
77B TRP* 3.1 20.7 - - - -
78B GLY* 1.3 71.9 + - - -
80B THR* 1.3 65.6 + - - +
81B LYS* 4.5 15.9 - - + +
148B VAL* 3.8 17.9 - - + -
149B ILE 3.4 3.8 - - - +
150B HIS* 2.6 40.9 + - + +
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 4.3 7.6 - - + -
64B ASP 3.5 2.9 - - - -
65B LEU* 3.7 20.3 - - + +
67B ILE* 5.7 0.2 - - - +
79B THR* 1.3 71.7 - - - +
81B LYS* 1.3 70.2 + - - +
82B VAL* 4.3 8.7 - - + +
147B VAL 3.3 2.3 - - - +
148B VAL* 3.3 1.9 - - - -
149B ILE* 2.8 43.0 + - + +
151B TYR* 3.4 18.0 + - - -
191B PHE* 3.6 10.4 - - - +
192B PRO* 3.5 35.4 - - + +
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Residues in contact with LYS 81 (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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62B HIS* 3.9 1.2 - - - +
63B TYR* 3.3 1.2 - - - -
64B ASP* 2.5 67.6 + - + +
79B THR* 4.5 15.7 - - + +
80B THR* 1.3 74.6 - - - +
82B VAL* 1.3 59.2 + - - +
83B GLU* 4.1 2.0 + - + +
108B ARG* 3.4 32.1 - - - +
146B THR* 4.2 13.7 - - + -
147B VAL 3.2 7.9 - - - +
148B VAL* 3.9 18.4 - - + -
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Residues in contact with VAL 82 (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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60B PRO* 3.8 17.5 - - + -
62B HIS 3.4 4.9 - - - +
63B TYR* 3.8 27.8 - - + +
80B THR* 4.5 9.4 - - + -
81B LYS* 1.3 71.9 - - - +
83B GLU* 1.3 67.7 + - - +
84B ILE* 3.6 23.5 + - + +
95B LEU* 4.8 8.1 - - + -
146B THR* 4.3 0.7 - - - -
147B VAL* 2.7 59.0 + - + +
149B ILE* 5.6 1.1 - - + -
192B PRO 5.9 0.4 - - - +
193B CYS* 6.4 0.2 - - - -
194B PHE* 3.9 10.8 - - + -
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Residues in contact with GLU 83 (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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60B PRO* 3.5 0.9 - - - +
61B VAL* 2.8 44.0 + - + +
62B HIS* 2.6 43.9 + - + +
81B LYS* 5.3 1.6 - - + +
82B VAL* 1.3 72.8 - - - +
84B ILE* 1.3 63.3 + - - +
144B PRO* 6.4 1.8 - - + -
145B TYR 3.5 6.5 - - - +
146B THR* 3.4 24.0 - - + +
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Residues in contact with ILE 84 (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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58B VAL* 4.2 14.8 - - + -
59B ILE 3.3 10.3 - - - +
60B PRO* 3.9 9.2 - - + -
61B VAL* 4.1 2.7 - - - +
82B VAL* 3.7 24.9 - - + +
83B GLU* 1.3 81.7 - - - +
85B THR* 1.3 73.5 + - - +
93B ILE* 3.5 34.5 - - + -
139B LEU* 4.1 12.8 - - + -
144B PRO* 3.6 1.7 - - - +
145B TYR* 2.7 46.5 + - + +
147B VAL* 3.9 10.5 - - + -
194B PHE* 4.0 12.3 - - + -
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 3.9 2.4 - - - +
59B ILE* 3.1 42.5 + - + +
61B VAL* 4.9 12.1 - - + -
84B ILE* 1.3 84.9 - - - +
86B ALA* 1.3 64.1 + - - +
87B SER 4.0 0.7 + - - -
139B LEU* 5.8 0.2 - - - -
142B GLY* 4.8 10.8 - - - +
143B LEU 4.0 18.4 - - - +
144B PRO* 4.2 10.3 - - + -
145B TYR* 5.4 0.9 - - - -
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Residues in contact with ALA 86 (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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57B TYR 3.5 8.3 - - - +
58B VAL* 4.4 5.2 - - + +
85B THR* 1.3 77.2 - - - +
87B SER* 1.3 55.2 + - - +
88B GLN 3.1 23.6 - - - +
90B THR* 4.1 15.0 - - + -
139B LEU* 4.5 21.7 - - + +
140B LEU 4.7 6.3 + - - +
141B VAL* 3.4 5.5 - - - +
142B GLY* 3.2 24.8 + - - -
143B LEU 4.6 3.8 + - - -
145B TYR* 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