Contacts of the strand formed by residues 114 - 121 (chain B) in PDB entry 4QYP
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 LYS 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A THR 5.0 4.9 + - - -
57A PHE 3.8 18.0 + - - +
58A ARG* 6.2 0.2 - - - -
8B TRP* 3.6 5.2 - - - -
11B GLU* 2.7 43.2 + - - +
110B ILE* 3.4 6.6 - - - +
111B GLU 2.9 35.8 + - - +
112B GLY 3.1 1.4 + - - -
113B ASP* 1.3 91.9 - - + +
115B LEU* 1.3 60.5 + - - +
116B TYR* 3.7 26.8 - - + +
129B VAL* 4.0 6.5 - - + -
130B PHE 3.2 11.7 - - - +
131B LYS* 4.4 7.4 - - + -
56C THR* 4.6 4.8 - - - +
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Residues in contact with LEU 115 (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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4B GLN* 4.8 1.1 - - + +
8B TRP* 3.4 37.3 - - + +
40B LYS* 4.9 3.8 - - + -
42B ILE* 3.7 30.3 - - + -
108B GLN* 4.0 24.7 - - + +
109B TRP 3.6 3.8 - - - +
110B ILE* 3.9 14.4 - - + -
114B LYS* 1.3 72.4 - - - +
116B TYR* 1.3 75.1 + - - +
117B LEU* 4.2 3.4 - - + +
129B VAL* 3.4 4.2 - - - +
130B PHE* 2.8 59.2 + - + +
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Residues in contact with TYR 116 (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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57A PHE 4.7 1.7 + - - -
58A ARG* 4.4 23.1 - - + +
59A ASN 4.8 1.0 + - - -
76A SER* 5.7 1.8 - - - -
107B LYS 3.9 0.3 - - - +
108B GLN* 3.3 7.3 - - - +
109B TRP* 2.8 81.4 + + + +
111B GLU* 3.7 30.6 + - + +
114B LYS* 3.7 38.6 - - + +
115B LEU* 1.3 76.2 - - - +
117B LEU* 1.4 61.0 + - - +
128B GLN 3.5 3.1 - - - +
129B VAL* 3.8 30.6 - - + +
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Residues in contact with LEU 117 (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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40B LYS* 3.5 27.8 - - + +
106B TRP* 4.0 26.2 - - + -
107B LYS 3.4 14.6 - - - +
108B GLN* 3.7 18.6 - - + +
109B TRP* 4.9 1.8 - - - -
115B LEU* 4.3 10.5 - - + -
116B TYR* 1.4 74.6 - - - +
118B GLU* 1.3 59.2 + - - +
119B LEU* 4.0 15.7 - - + -
126B CYS 3.7 1.0 - - - +
127B ARG* 3.5 2.9 - - - +
128B GLN* 2.8 63.9 + - + +
130B PHE* 4.4 0.2 - - + -
201B RET 4.0 13.5 - - + -
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Residues in contact with GLU 118 (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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73A TYR* 4.0 6.3 + - - -
79A ASN* 2.8 31.1 - - - +
106B TRP* 3.0 6.2 - - - +
107B LYS* 2.8 65.9 + - + +
109B TRP* 4.2 13.5 - - + -
117B LEU* 1.3 73.7 - - - +
119B LEU* 1.3 59.8 + - - +
120B THR* 4.1 13.8 + - + +
125B VAL* 3.5 27.1 - - + +
126B CYS 3.4 3.8 - - - +
127B ARG* 4.2 14.5 + - + +
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Residues in contact with LEU 119 (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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16B PHE* 4.5 1.6 - - + -
19B TYR* 3.7 32.0 - - + +
105B GLY 3.7 2.5 - - - -
106B TRP* 4.0 18.8 - - + -
117B LEU* 4.0 17.0 - - + -
118B GLU* 1.3 74.8 - - - +
120B THR* 1.3 62.8 + - - +
125B VAL* 3.4 3.3 - - - -
126B CYS* 2.8 50.3 + - + +
128B GLN* 3.8 33.2 - - + +
201B RET 3.9 37.9 - - + -
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Residues in contact with THR 120 (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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19B TYR* 3.7 7.5 - - - -
103B ASN* 3.1 25.5 + - - +
104B ARG* 3.3 3.1 - - - +
105B GLY* 3.0 37.9 + - - +
106B TRP* 5.0 0.8 - - - -
118B GLU* 4.2 22.4 - - + +
119B LEU* 1.3 80.3 - - - +
121B CYS* 1.4 65.1 + - - +
124B GLN 3.4 6.1 - - - -
125B VAL* 3.7 21.3 - - + -
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Residues in contact with CYS 121 (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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19B TYR* 3.9 17.6 - - + -
22B ALA* 3.6 22.9 - - + +
23B LEU* 3.8 21.5 - - + -
101B LYS* 3.7 39.0 - - - -
102B GLU 4.2 0.4 - - - -
103B ASN 3.5 4.7 - - - -
104B ARG* 4.2 5.4 - - + +
120B THR* 1.4 78.2 - - - +
122B GLY* 1.3 67.8 - - - +
123B ASP 3.2 0.5 + - - -
124B GLN* 3.0 26.1 + - - +
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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