Contacts of the strand formed by residues 130 - 139 (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 GLN 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B PHE* 3.9 16.8 - - + -
49B TRP* 3.5 22.7 - - - +
51B LYS 3.3 20.0 + - - -
52B ILE* 3.3 16.6 + - - +
54B LEU* 3.6 15.9 - - + +
94B ILE* 4.0 7.4 - - + -
95B LEU 3.3 9.4 - - - +
96B HIS* 3.9 12.4 + - + -
97B SER 4.4 1.1 - - - +
124B GLU* 4.8 0.2 - - - +
125B HIS 3.0 25.8 + - - +
126B PRO* 4.9 0.9 - - - +
128B GLN* 3.0 39.1 + - + +
129B GLU* 1.3 79.0 - - - +
131B ILE* 1.3 69.8 + - - +
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Residues in contact with ILE 131 (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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47B PHE* 3.9 6.5 - - - -
93B ILE 3.8 0.5 - - - +
94B ILE* 3.6 2.6 - - - +
95B LEU* 2.8 61.8 + - + +
97B SER* 3.7 24.7 - - - +
102B ILE* 3.1 36.1 - - + -
122B VAL* 4.9 1.1 - - + -
123B LEU 3.0 14.6 - - - +
124B GLU* 3.9 14.1 - - + -
130B GLN* 1.3 81.0 - - - +
132B ALA* 1.3 59.9 + - - +
133B LEU* 4.4 13.5 - - + -
149B ILE* 4.5 3.1 - - + -
192B PRO* 4.5 5.2 - - + -
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Residues in contact with ALA 132 (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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47B PHE* 3.6 15.8 - - + -
48B PRO* 3.8 15.9 - - + -
92B THR* 4.3 0.9 - - + -
93B ILE 3.4 4.5 - - - -
94B ILE* 3.7 21.8 - - + -
121B GLN 3.5 1.0 - - - +
122B VAL* 3.4 0.5 - - - -
123B LEU* 2.5 41.1 + - + +
131B ILE* 1.3 73.5 - - - +
133B LEU* 1.3 68.3 + - - +
134B LEU* 3.9 10.5 - - + -
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Residues in contact with LEU 133 (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 SER 3.9 0.3 - - - +
92B THR* 3.4 3.6 - - - -
93B ILE* 2.8 47.9 + - + +
95B LEU* 4.4 13.9 - - + -
105B ALA* 4.2 3.8 - - + -
120B LEU* 3.9 24.1 - - + +
121B GLN 3.4 2.5 - - - -
122B VAL* 3.5 27.6 - - + -
131B ILE* 4.4 17.0 - - + -
132B ALA* 1.3 82.0 - - - +
134B LEU* 1.3 62.9 + - - +
147B VAL* 3.8 22.9 - - + -
149B ILE* 3.8 25.8 - - + -
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Residues in contact with LEU 134 (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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48B PRO* 4.7 4.3 - - + -
91B SER 3.5 4.7 - - - +
92B THR* 3.7 26.0 - - + +
120B LEU* 3.3 10.2 - - - -
121B GLN* 2.9 60.7 + - + +
123B LEU* 3.8 29.4 - - + -
132B ALA* 3.9 9.9 - - + -
133B LEU* 1.3 78.6 - - - +
135B ALA* 1.3 61.5 + - - +
136B PRO* 4.2 2.1 - - - +
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Residues in contact with ALA 135 (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 SER* 2.8 29.0 + - - +
93B ILE* 6.3 0.2 - - + -
107B LEU* 4.0 16.6 - - + -
120B LEU* 3.8 16.4 - - + -
133B LEU 4.2 0.4 + - - -
134B LEU* 1.3 73.5 - - - +
136B PRO* 1.4 73.3 - - + +
137B GLU 3.3 16.2 + - - +
139B LEU* 4.4 8.5 - - + -
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Residues in contact with PRO 136 (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 SER* 5.5 0.7 - - - -
118B GLU* 4.6 22.4 - - + +
119B PRO* 3.9 21.1 - - + +
120B LEU* 5.2 0.2 - - + -
134B LEU 4.2 2.0 - - - +
135B ALA* 1.4 86.7 - - + +
137B GLU* 1.3 59.0 + - + +
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Residues in contact with GLU 137 (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 SER* 4.2 2.0 - - - -
107B LEU* 5.5 1.2 - - - +
135B ALA* 3.4 23.1 - - - +
136B PRO* 1.3 79.2 - - + +
138B PRO* 1.3 77.8 - - + +
139B LEU* 4.6 0.7 - - - +
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Residues in contact with PRO 138 (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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89B PRO* 5.0 6.3 - - + -
90B THR* 3.6 22.9 - - - +
91B SER* 3.9 10.4 - - - +
137B GLU* 1.3 91.9 - - + +
139B LEU* 1.3 66.4 - - - +
140B LEU* 3.7 10.8 + - + +
145B TYR* 4.3 2.4 + - - -
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Residues in contact with LEU 139 (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* 6.1 1.3 - - + -
84B ILE* 4.1 20.2 - - + -
86B ALA* 4.5 20.3 - - + +
88B GLN 4.9 0.7 - - - +
89B PRO* 3.8 22.3 - - - +
90B THR* 2.8 33.9 + - + +
91B SER* 4.4 1.3 - - - -
93B ILE* 4.5 17.0 - - + -
107B LEU* 4.1 17.7 - - + -
135B ALA* 4.4 13.0 - - + -
138B PRO* 1.3 76.1 - - - +
140B LEU* 1.3 63.7 + - - +
141B VAL 3.8 1.2 + - - -
145B TYR* 3.4 52.5 - - + -
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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