Contacts of the strand formed by residues 311 - 320 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C PHE* 3.4 10.8 - - + -
83C PRO* 3.0 24.4 - - - +
84C PHE* 2.7 53.2 + + + +
85C SER* 4.7 0.2 - - - -
86C ASN* 3.5 29.6 - - + -
91C LEU* 3.9 10.8 - - + -
112C LEU* 3.8 31.6 - - + -
113C PHE 3.6 3.6 - - - -
129C ASN* 3.4 31.0 - - + -
130C ILE* 3.9 13.9 - - + -
308C TYR* 3.6 27.4 - + + -
310C ASN* 1.3 76.3 - - - +
312C GLY* 1.3 58.0 + - - +
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Residues in contact with GLY 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C SER* 3.2 7.6 - - - -
81C PHE* 2.9 43.0 + - - +
83C PRO* 4.4 0.4 - - - -
113C PHE 2.9 7.8 + - - -
115C ASN* 3.7 27.3 - - - +
310C ASN* 3.5 2.8 + - - -
311C PHE* 1.3 74.5 - - - +
313C VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C SER* 3.4 33.4 - - - +
79C ALA 3.3 10.5 - - - +
80C SER* 4.4 4.0 - - - -
81C PHE* 3.6 6.2 - - - -
111C LYS 3.7 0.3 - - - +
112C LEU* 3.5 3.1 - - - -
113C PHE* 2.7 65.2 + - + +
114C PRO 3.8 9.0 - - - +
115C ASN* 5.2 1.3 - - - +
117C LEU* 3.6 16.8 - - + +
119C GLN* 3.8 18.2 - - + +
312C GLY* 1.3 80.5 - - - +
314C LEU* 1.3 62.4 + - - +
315C GLY 4.1 0.2 - - - -
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Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE* 4.7 13.7 - - + -
37C TRP* 4.1 14.3 - - + -
78C SER* 3.3 4.0 - - - -
79C ALA* 2.9 38.2 + - + +
81C PHE* 3.5 12.2 - - + -
93C VAL* 5.0 3.1 - - + -
110C VAL* 3.6 33.7 - - + -
111C LYS 3.3 9.0 - - - +
112C LEU* 4.1 9.4 - - + +
313C VAL* 1.3 73.0 - - - +
315C GLY* 1.3 66.8 + - - +
316C LEU* 4.7 0.7 - - + +
330C PHE* 4.0 25.1 - - + -
332C ILE* 3.8 27.8 - - + -
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Residues in contact with GLY 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LEU 3.6 7.0 - - - -
78C SER* 3.8 8.3 - - - -
109C TYR 4.4 0.2 - - - +
110C VAL* 3.6 5.7 - - - -
111C LYS* 2.8 40.1 + - - +
113C PHE* 4.1 5.7 - - - -
122C MET* 4.1 11.9 - - - -
313C VAL 4.1 0.4 - - - -
314C LEU* 1.3 77.1 - - - +
316C LEU* 1.3 65.4 + - - -
317C ASP* 3.8 3.3 + - - -
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C TRP* 4.1 13.5 - - + -
49C PHE* 3.9 32.5 - - + -
66C LEU* 3.7 30.3 - - + -
75C TYR 3.8 0.7 - - - -
76C ALA* 3.3 5.9 + - - -
77C LEU* 2.8 35.5 + - + +
109C TYR 4.2 10.3 - - - +
110C VAL* 3.9 24.9 - - + -
122C MET* 4.1 0.4 - - - -
314C LEU* 4.8 0.7 - - + -
315C GLY* 1.3 70.7 - - - -
317C ASP* 1.3 59.1 + - - +
318C LEU* 4.1 7.4 - - + -
327C PHE* 4.1 28.3 - - + -
330C PHE* 4.1 11.4 - - + -
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Residues in contact with ASP 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C PHE* 6.1 1.0 - - - -
75C TYR 3.3 8.9 - - - +
76C ALA* 5.2 0.9 - - - -
109C TYR* 3.5 19.8 + - - -
111C LYS* 3.5 26.8 + - + +
113C PHE* 4.6 2.3 - - - -
122C MET* 3.7 23.3 - - + +
123C HIS* 2.8 36.0 - - - +
124C GLY* 3.5 18.3 + - - -
315C GLY 3.8 3.3 + - - -
316C LEU* 1.3 73.5 - - - +
318C LEU* 1.3 66.1 + - - +
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C PHE* 5.2 1.1 - - + -
68C THR* 4.7 4.9 - - + -
74C PHE* 3.3 9.1 - - - -
75C TYR* 2.8 55.0 + - + -
107C GLY* 3.8 21.5 - - - +
109C TYR* 3.6 43.7 - - + +
316C LEU* 4.5 7.9 - - + -
317C ASP* 1.3 83.2 + - - +
319C TRP* 1.3 61.7 + - - +
320C GLN* 3.9 20.4 - - + +
327C PHE* 3.9 22.4 - - + -
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Residues in contact with TRP 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ALA* 3.4 33.2 - - + -
73C ARG* 3.3 37.2 - - - -
74C PHE* 3.6 42.4 - + + -
105C CYS* 4.8 14.0 - - - -
106C GLY* 3.2 4.6 - - - -
107C GLY 3.0 25.7 + - - +
109C TYR* 4.8 3.4 + - - +
318C LEU* 1.3 75.6 - - - +
320C GLN* 1.3 71.0 + - - +
321C VAL* 3.7 24.4 - - + +
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Residues in contact with GLN 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C THR* 2.5 35.4 + - + +
70C GLN 5.2 0.4 - - - +
72C ALA* 3.0 5.4 + - - -
73C ARG 3.0 31.5 + - - -
75C TYR* 4.1 12.6 - - + -
99C HIS* 4.5 0.2 - - - -
103C ILE* 3.8 12.2 - - + +
105C CYS 3.9 3.8 - - - -
106C GLY* 4.1 5.6 - - - -
107C GLY 3.1 20.2 + - - -
318C LEU* 3.9 11.7 - - + +
319C TRP* 1.3 85.4 - - - +
321C VAL* 1.3 66.3 + - - +
322C LYS 3.9 2.6 - - - +
323C SER* 3.6 11.4 - - - -
325C THR* 2.9 30.2 + - - +
327C PHE* 5.0 0.4 - - - -
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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