Contacts of the strand formed by residues 311 - 320 (chain F) in PDB entry 5LK5
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 PHE 311 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81F PHE* 3.4 10.8 - - + -
83F PRO* 3.0 23.6 - - - +
84F PHE* 2.7 49.5 + + + +
85F SER* 4.7 0.2 - - - -
86F ASN* 3.4 29.6 - - + -
91F LEU* 3.9 11.7 - - + -
112F LEU* 3.8 31.4 - - + -
113F PHE 3.6 4.0 - - - +
129F ASN* 3.4 31.2 - - + -
130F ILE* 3.9 13.9 - - + -
308F TYR* 3.6 27.6 - + + -
310F ASN* 1.3 78.2 - - - +
312F GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F SER* 3.2 7.1 - - - -
81F PHE* 2.9 41.9 + - - +
83F PRO* 4.4 0.9 - - - -
113F PHE 2.9 7.4 + - - -
115F ASN* 3.7 24.0 - - - +
310F ASN* 3.5 2.8 + - - -
311F PHE* 1.3 74.3 - - - +
313F VAL* 1.3 66.9 + - - +
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Residues in contact with VAL 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F SER* 3.4 33.9 - - - +
79F ALA 3.3 10.5 - - - +
80F SER* 4.1 9.6 - - - -
81F PHE* 3.6 8.7 - - - -
111F LYS 3.7 0.3 - - - +
112F LEU* 3.5 3.1 - - - -
113F PHE* 2.7 45.7 + - + +
114F PRO 4.6 7.4 - - - +
115F ASN* 4.7 6.3 - - - +
117F LEU* 4.1 20.6 - - + +
119F GLN* 4.1 18.2 - - + +
312F GLY* 1.3 85.1 - - - +
314F LEU* 1.3 63.1 + - - +
315F GLY 4.3 0.7 - - - +
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Residues in contact with LEU 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F PHE* 4.7 12.8 - - + -
37F TRP* 4.1 14.9 - - + -
78F SER* 3.3 1.4 - - - -
79F ALA* 2.9 37.1 + - + +
81F PHE* 3.5 12.6 - - + -
93F VAL* 4.9 3.8 - - + -
94F GLN 6.2 0.2 - - - +
95F PHE* 6.1 0.4 - - + -
110F VAL* 4.1 20.0 - - + -
111F LYS 3.3 8.1 - - - +
112F LEU* 4.1 10.5 - - + +
313F VAL* 1.3 74.4 - - - +
315F GLY* 1.3 67.1 + - - +
316F LEU* 4.7 1.1 - - + +
330F PHE* 4.0 37.0 - - + -
332F ILE* 3.8 26.7 - - + -
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Residues in contact with GLY 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F LEU 3.6 7.2 - - - -
78F SER* 3.8 8.3 - - - -
110F VAL* 3.6 6.8 - - - +
111F LYS* 2.8 40.3 + - - +
113F PHE* 4.1 4.6 - - - -
122F MET* 4.1 12.8 - - - -
313F VAL 4.0 0.8 - - - -
314F LEU* 1.3 76.9 - - - +
316F LEU* 1.3 64.2 + - - -
317F ASP* 3.7 3.4 + - - -
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Residues in contact with LEU 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F TRP* 4.1 11.0 - - + -
49F PHE* 3.8 31.3 - - + -
66F LEU* 3.7 29.2 - - + -
75F TYR 3.6 1.2 - - - +
76F ALA* 3.3 6.8 + - - -
77F LEU* 2.8 34.2 + - + +
109F TYR 4.2 9.2 - - - +
110F VAL* 3.8 28.0 - - + -
122F MET* 4.1 0.2 - - - -
314F LEU* 4.3 0.4 + - + -
315F GLY* 1.3 70.8 - - - +
317F ASP* 1.3 58.4 + - - +
318F LEU* 4.1 7.2 - - + -
327F PHE* 4.1 21.8 - - + -
330F PHE* 4.0 18.6 - - + -
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Residues in contact with ASP 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F PHE* 5.4 1.6 - - - -
75F TYR 3.3 12.3 - - - +
76F ALA* 3.9 6.1 - - - +
109F TYR* 3.5 10.2 + - - -
111F LYS* 3.5 42.4 + - + +
113F PHE* 5.4 0.2 - - - -
122F MET* 4.0 17.7 - - + -
123F HIS* 3.2 27.2 - - - +
124F GLY* 3.2 26.8 + - - -
315F GLY 3.7 3.3 + - - -
316F LEU* 1.3 74.7 - - - +
318F LEU* 1.3 65.2 + - - +
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Residues in contact with LEU 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F PHE* 5.2 0.9 - - + -
68F THR* 4.7 5.6 - - + -
73F ARG 4.0 0.2 - - - +
74F PHE* 3.3 9.7 - - - -
75F TYR* 2.8 53.5 + - + +
107F GLY* 3.8 21.3 - - - +
109F TYR* 3.6 44.9 - - + +
316F LEU* 4.5 8.1 - - + -
317F ASP* 1.3 82.4 - - - +
319F TRP* 1.3 62.7 + - - +
320F GLN* 3.9 20.6 - - + +
327F PHE* 3.9 22.7 - - + -
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Residues in contact with TRP 319 (chain F).
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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72F ALA* 3.5 32.3 - - + -
73F ARG* 3.3 38.6 - - - -
74F PHE* 3.6 42.0 - + + -
105F CYS* 4.8 14.2 - - - -
106F GLY* 3.3 5.3 - - - -
107F GLY* 3.0 26.2 + - - +
109F TYR* 4.8 3.4 + - - +
318F LEU* 1.3 76.1 - - - +
320F GLN* 1.3 71.0 + - - +
321F VAL* 3.7 24.6 - - + +
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Residues in contact with GLN 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F THR* 2.5 34.8 + - + +
70F GLN 4.7 0.8 - - - +
72F ALA* 3.0 6.6 + - - -
73F ARG 3.0 31.3 + - - -
75F TYR* 4.2 11.9 - - + -
103F ILE* 3.7 12.2 - - + +
105F CYS 3.9 4.3 - - - -
106F GLY* 4.1 5.8 - - - -
107F GLY 3.1 20.6 + - - -
318F LEU* 3.9 10.8 - - + +
319F TRP* 1.3 85.8 - - - +
321F VAL* 1.3 66.2 + - - +
322F LYS 4.3 3.1 - - - +
323F SER* 3.6 11.2 - - - -
325F THR* 2.9 29.8 + - - +
327F PHE* 5.0 0.8 - - - -
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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