Contacts of the strand formed by residues 121 - 128 (chain B) in PDB entry 6Q0V
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 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B TRP* 3.5 2.4 - - - -
113B GLU* 2.8 51.7 + - + +
119B LYS* 3.7 7.2 + - + +
120B LEU* 1.3 76.2 - - - +
122B LEU* 1.3 71.0 + - - +
123B VAL* 3.4 2.3 + - + +
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Residues in contact with LEU 122 (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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73B PHE* 3.6 33.9 - - + -
110B TYR* 4.0 27.6 - - + -
111B TRP 3.5 11.4 - - - +
112B TRP* 3.7 25.8 - - + -
121B LYS* 1.3 79.4 + - - +
123B VAL* 1.3 60.9 + - - +
124B ARG 3.3 30.5 - - - +
125B GLN* 4.4 12.6 - - + +
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Residues in contact with VAL 123 (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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88B ARG* 6.3 0.7 - - - +
89B TYR* 4.0 14.8 - - + +
111B TRP* 2.9 16.5 + - + +
113B GLU* 3.8 22.9 - - + +
121B LYS* 3.5 16.2 - - + +
122B LEU* 1.3 74.8 - - - +
124B ARG* 1.4 62.8 + - - +
188B PRO* 3.6 33.0 - - + -
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Residues in contact with ARG 124 (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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109B LEU 4.3 0.2 - - - -
110B TYR* 3.2 4.8 - - - -
111B TRP* 2.8 62.5 + - + -
122B LEU* 3.3 7.5 - - - +
123B VAL* 1.4 79.1 + - - +
125B GLN* 1.3 61.8 + - - +
126B VAL* 4.0 11.2 - - + -
186B ALA 2.7 39.5 + - - -
187B VAL 3.5 2.0 - - - -
188B PRO* 3.7 28.8 - - + +
189B PRO* 3.9 1.4 - - - +
210B GLN* 3.4 24.7 + - - +
214B HIS 2.8 30.7 + - - -
422C LEU* 3.6 30.4 - - + +
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Residues in contact with GLN 125 (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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73B PHE* 5.6 1.9 - - - -
108B HIS* 3.9 25.3 + - + -
109B LEU 3.4 5.4 - - - +
110B TYR* 3.3 38.9 + - + -
122B LEU* 4.4 13.7 - - + +
124B ARG* 1.3 72.9 - - - +
126B VAL* 1.3 65.4 + - - +
422C LEU* 5.1 2.9 - - - +
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Residues in contact with VAL 126 (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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108B HIS* 3.2 11.7 - - - +
109B LEU* 2.9 52.7 + - + +
111B TRP* 3.8 18.8 - - + -
124B ARG* 4.0 11.9 - - + -
125B GLN* 1.3 78.6 - - - +
127B ARG* 1.3 58.9 - - - +
128B LEU* 3.6 2.4 + - + -
185B VAL* 3.8 15.7 - - + -
217B MET* 3.8 17.0 - - - -
422C LEU* 3.7 40.4 - - + +
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Residues in contact with ARG 127 (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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105B TYR 5.4 1.0 + - - -
106B ILE* 3.5 35.9 - - + +
107B TYR 3.6 6.1 - - - +
108B HIS* 3.8 22.6 - - + +
126B VAL* 1.3 70.8 - - - +
128B LEU* 1.3 74.5 + - - +
129B PHE 3.8 6.0 + - - -
130B GLN* 3.8 29.4 + - - +
131B ASP* 5.0 9.6 + - - +
132B GLU 5.1 8.9 + - - +
217B MET* 3.4 25.4 - - + +
219B HIS* 3.9 2.8 - - - -
422C LEU 5.1 2.6 + - - +
423C ARG 5.6 4.5 - - - +
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Residues in contact with LEU 128 (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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93B TYR* 5.2 0.7 - - + -
107B TYR* 2.8 33.3 + - + +
108B HIS 4.1 6.1 - - - +
109B LEU* 3.8 37.7 - - + +
126B VAL* 3.6 3.3 + - + +
127B ARG* 1.3 81.7 + - - +
129B PHE* 1.4 88.8 + - + +
134B ILE* 5.6 1.0 - - - +
140B LEU* 4.6 9.0 - - + -
154B VAL* 3.8 43.7 - - + -
183B SER* 4.2 7.6 - - - -
185B VAL* 4.1 19.1 - - + -
217B MET* 5.4 1.1 - - - -
219B HIS* 4.5 1.6 - - - -
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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