Contacts of the strand formed by residues 54 - 62 (chain V) in PDB entry 5L4K
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 MET 54 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44V HIS* 3.4 13.2 - - - -
53V VAL* 1.3 77.1 - - - +
55V GLY* 1.3 62.4 + - - +
56V LEU* 5.1 3.4 - - + -
75V MET* 3.3 51.8 + - + +
76V PRO 5.2 4.0 - - - +
77V GLN* 6.3 1.8 - - + -
82V VAL* 4.7 14.4 - - + -
83V SER 5.6 1.1 - - - +
84V VAL* 6.0 2.0 - - + -
87V VAL* 4.1 32.8 - - + -
111V TRP* 4.2 31.6 - - + -
112V TYR* 3.2 14.1 - - - +
113V HIS* 3.8 8.5 - - + +
129V THR* 6.0 1.8 - - + -
133V PHE* 5.0 7.6 - - + -
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Residues in contact with GLY 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54V MET* 1.3 82.4 - - - +
56V LEU* 1.3 65.5 + - - -
73V PHE 3.5 10.1 - - - -
74V ALA* 4.0 5.4 - - - -
75V MET* 4.8 0.2 - - - -
111V TRP* 3.3 5.5 - - - +
112V TYR* 2.9 49.5 + - - -
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Residues in contact with LEU 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54V MET* 5.1 1.8 - - + -
55V GLY* 1.3 78.9 - - - +
57V MET* 1.3 60.4 + - - +
58V LEU* 4.2 2.9 - - + -
72V VAL* 3.3 8.3 - - - +
73V PHE* 3.1 57.5 + - + -
74V ALA 4.6 0.8 + - - -
75V MET* 4.1 21.5 - - + +
92V GLN* 3.7 36.1 - - + +
96V LEU* 5.8 0.7 - - + -
108V VAL* 3.9 25.4 - - + -
110V GLY 3.8 6.3 - - - +
111V TRP* 4.6 2.5 - - + -
133V PHE* 3.9 31.6 - - + -
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Residues in contact with MET 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33V ILE* 6.3 0.9 - - - -
41V MET* 4.6 5.8 - - - +
56V LEU* 1.3 77.3 - - - +
58V LEU* 1.3 61.0 + - - +
69V VAL* 3.8 27.4 - - + -
71V ASP 3.8 3.4 - - - -
72V VAL* 3.7 13.0 - - + -
108V VAL* 3.5 5.2 - - - +
109V VAL* 3.0 34.2 + - + +
110V GLY* 2.9 33.9 + - - +
111V TRP 3.5 3.4 - - - +
112V TYR* 4.1 15.3 - - + -
141V VAL* 3.5 35.2 - - + +
143V VAL* 3.7 23.8 - - + -
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Residues in contact with LEU 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57V MET* 1.3 83.2 - - - +
59V GLY* 1.3 57.4 - - - +
69V VAL* 3.9 0.9 - - - -
70V ILE* 3.0 3.9 + - - -
71V ASP* 2.5 54.0 + - + +
72V VAL 5.8 0.2 - - - -
73V PHE* 3.4 38.1 - - + -
96V LEU* 4.0 16.6 - - + -
99V LEU* 3.7 23.1 - - + -
104V ARG* 6.2 1.8 - - - +
106V GLU* 4.0 18.8 - - + -
107V MET* 3.6 15.3 - - - +
108V VAL* 3.8 22.0 - - + -
109V VAL* 4.6 2.7 - - - -
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Residues in contact with GLY 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57V MET 4.3 0.2 + - - -
58V LEU* 1.3 76.7 - - - +
60V GLU* 1.3 76.7 + - - +
68V ARG 3.4 11.4 - - - -
69V VAL* 4.5 0.4 - - - -
70V ILE* 3.7 9.9 - - - -
106V GLU* 3.8 13.7 - - - +
107V MET* 3.3 24.3 + - - +
109V VAL* 3.9 6.9 - - - +
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Residues in contact with GLU 60 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59V GLY* 1.3 86.0 - - - +
61V PHE* 1.3 64.2 + - - +
62V VAL* 4.2 2.5 - - + -
67V VAL* 4.4 0.2 - - - -
68V ARG* 2.8 62.0 + - - +
70V ILE* 3.9 7.7 - - + +
105V PRO* 3.2 17.2 - - - +
106V GLU* 2.8 27.9 - - - +
107V MET* 4.2 11.4 + - - +
109V VAL* 4.1 6.3 - - - +
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Residues in contact with PHE 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29V GLU* 6.1 0.2 - - - -
60V GLU* 1.3 78.9 - - - +
62V VAL* 1.4 61.7 + - - +
63V ASP 4.0 8.0 + - - +
64V ASP* 3.9 35.7 - - + -
65V TYR 5.6 0.2 - - - -
66V THR 3.5 21.1 - - - -
67V VAL* 4.3 15.3 - - + -
107V MET* 3.8 21.5 - - + +
109V VAL* 4.5 8.1 - - + -
139V ARG* 3.3 46.7 - - + -
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Residues in contact with VAL 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540N GLN* 3.9 23.1 - - + +
541N HIS* 6.3 1.3 - - - -
32V TYR* 5.8 0.9 - - + -
60V GLU* 4.4 1.3 + - + -
61V PHE* 1.4 74.2 - - - +
63V ASP* 1.3 83.6 + - + +
64V ASP* 2.9 6.6 + - - -
66V THR* 3.1 44.3 + - + +
68V ARG* 3.3 39.7 - - + +
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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