Contacts of the strand formed by residues 122 - 126 (chain L) in PDB entry 2QJK
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 TRP 122 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54L VAL* 3.2 43.3 - - + -
57L VAL* 4.2 8.5 - - + -
74L ILE* 4.4 13.5 - - + -
75L ARG 4.1 7.0 - - - -
76L ARG* 3.4 52.5 - - + +
115L THR* 3.6 4.1 - - - -
116L LEU* 3.1 33.0 + - + +
117L ASP* 2.9 25.6 + - + +
120L GLY 3.5 0.4 - - - -
121L GLU* 1.3 87.2 + - + +
123L LEU* 1.3 63.0 + - - +
124L VAL* 3.7 4.3 + - + -
178L PHE* 3.4 43.8 - + + -
184L ILE* 4.9 1.6 - - + -
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Residues in contact with LEU 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L PHE 3.7 2.1 - - - +
74L ILE* 3.5 2.6 - - - +
75L ARG* 3.0 40.7 + - + +
77L ARG* 4.2 18.4 - - + +
114L ARG* 3.4 28.7 - - + +
115L THR* 4.7 4.5 - - + -
121L GLU 3.8 1.4 + - - -
122L TRP* 1.3 70.9 - - - +
124L VAL* 1.3 63.4 + - - +
125L MET* 3.7 20.4 - - + -
147L TRP* 3.5 32.1 - - + -
158L SER 3.5 19.5 - - - +
159L ALA* 3.8 22.2 - - - +
173L ILE* 5.4 0.4 - - + -
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Residues in contact with VAL 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72L ILE* 4.9 2.5 - - + -
73L PHE 3.4 4.3 - - - +
74L ILE* 3.5 34.8 - - + -
114L ARG 4.7 2.2 + - - +
116L LEU* 4.1 25.2 - - + +
122L TRP* 3.7 5.9 + - + +
123L LEU* 1.3 79.5 - - - +
125L MET* 1.3 65.7 + - - +
173L ILE* 2.9 29.8 - - - +
174L PRO* 4.3 9.6 - - + -
176L ALA* 4.1 13.0 - - + -
184L ILE* 4.2 9.2 - - + -
186L LEU* 3.9 24.5 - - + -
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Residues in contact with MET 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72L ILE* 3.6 4.8 - - - -
73L PHE* 2.7 51.4 + - + +
114L ARG* 3.9 5.6 - - - -
123L LEU* 3.7 16.6 - - + +
124L VAL* 1.3 77.5 - - - +
126L TRP* 1.3 59.0 + - - +
147L TRP* 3.3 48.7 - - + -
160L GLY* 3.8 13.2 - - - -
171L LEU* 3.5 39.0 - - + -
172L PRO 3.3 17.5 - - - +
173L ILE* 4.2 6.5 - - + -
174L PRO* 3.8 8.3 - - - -
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Residues in contact with TRP 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L PHE* 3.4 50.0 - + - -
68L LEU* 3.9 11.9 - - + -
70L LYS* 3.3 33.4 - - + -
71L PRO 3.4 12.3 - - - -
72L ILE* 3.2 26.9 - - + -
125L MET* 1.3 70.8 - - - +
127L GLY* 1.3 52.3 + - - +
128L VAL* 2.6 29.0 + - + +
171L LEU* 3.8 19.6 - - - +
172L PRO* 2.8 47.9 + - + +
174L PRO* 3.4 28.0 - - + +
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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