Contacts of the strand formed by residues 311 - 320 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81I PHE* 3.4 10.7 - - + -
83I PRO* 3.0 24.3 - - - +
84I PHE* 2.7 52.1 + + + +
85I SER* 4.7 0.2 - - - -
86I ASN* 3.4 30.3 - - + -
91I LEU* 3.9 20.2 - - + -
112I LEU* 3.8 29.8 - - + -
113I PHE 3.6 4.7 - - - +
129I ASN* 3.4 30.5 - - + -
130I ILE* 3.9 5.4 - - + -
308I TYR* 3.6 27.1 - + + -
310I ASN* 1.3 76.5 - - - +
312I GLY* 1.3 57.0 + - - +
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Residues in contact with GLY 312 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80I SER* 3.2 6.2 - - - -
81I PHE* 2.9 42.5 + - - +
83I PRO* 4.4 0.9 - - - -
113I PHE 2.9 7.4 + - - -
115I ASN* 3.6 24.8 + - - +
310I ASN* 3.5 2.2 + - - -
311I PHE* 1.3 74.3 - - - +
313I VAL* 1.3 66.8 + - - +
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Residues in contact with VAL 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I SER* 3.6 31.6 - - - +
79I ALA 3.3 11.7 - - - +
80I SER* 4.1 6.3 - - - -
81I PHE* 3.6 7.1 - - - -
111I LYS 3.7 0.5 - - - +
112I LEU* 3.5 3.5 - - - +
113I PHE* 2.7 46.1 + - + +
114I PRO 4.6 6.3 - - - +
115I ASN* 4.6 7.4 - - - +
117I LEU* 4.1 20.6 - - + +
119I GLN* 4.0 22.9 - - + +
312I GLY* 1.3 85.5 - - - +
314I LEU* 1.3 63.8 + - - +
315I GLY 4.3 0.4 - - - +
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Residues in contact with LEU 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I PHE* 3.8 24.7 - - + -
37I TRP* 4.1 13.8 - - + -
78I SER* 3.4 1.6 - - - -
79I ALA 2.9 38.2 + - - +
81I PHE* 3.5 11.9 - - + -
93I VAL* 4.9 3.4 - - + -
110I VAL* 4.0 26.0 - - + -
111I LYS 3.4 3.4 - - - +
112I LEU* 3.3 26.9 - - + -
313I VAL* 1.3 73.0 - - - +
315I GLY* 1.3 59.4 + - - +
316I LEU* 5.7 0.4 - - + -
330I PHE* 3.2 40.6 - - + -
332I ILE* 3.9 11.0 - - + -
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Residues in contact with GLY 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I LEU 3.6 7.2 - - - -
78I SER* 3.7 10.3 - - - -
110I VAL* 3.6 6.4 - - - +
111I LYS* 2.8 41.1 + - - +
113I PHE* 4.1 6.0 - - - -
122I MET* 4.1 10.1 - - - -
313I VAL 4.1 1.4 - - - -
314I LEU* 1.3 75.9 - - - +
316I LEU* 1.3 64.4 + - - -
317I ASP* 3.7 3.2 + - - -
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Residues in contact with LEU 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I TRP* 4.1 12.1 - - + -
49I PHE* 3.9 31.9 - - + -
66I LEU* 3.8 29.2 - - + -
75I TYR 3.6 0.9 - - - +
76I ALA* 3.3 6.4 + - - -
77I LEU* 2.8 35.2 + - + +
109I TYR 4.2 8.7 - - - +
110I VAL* 3.7 28.3 - - + -
122I MET* 3.6 0.6 - - - +
314I LEU* 5.7 0.7 - - + -
315I GLY* 1.3 71.0 - - - +
317I ASP* 1.3 58.9 + - - +
318I LEU* 4.1 7.4 - - + -
327I PHE* 4.1 22.7 - - + -
330I PHE* 4.1 20.4 - - + -
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Residues in contact with ASP 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I PHE* 5.4 1.6 - - - -
75I TYR 3.3 12.3 - - - +
76I ALA* 3.9 6.4 - - - +
109I TYR* 3.5 18.7 + - - -
111I LYS* 3.5 32.2 + - + +
113I PHE* 5.1 0.6 - - + -
122I MET* 4.0 18.4 - - + -
123I HIS* 3.2 27.8 + - - +
124I GLY* 3.2 27.2 + - - -
315I GLY 3.7 2.9 + - - -
316I LEU* 1.3 75.6 - - - +
318I LEU* 1.3 65.4 + - - +
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Residues in contact with LEU 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I PHE* 5.2 0.7 - - + -
68I THR* 4.8 5.4 - - + -
73I ARG 4.0 0.3 - - - +
74I PHE* 3.3 8.6 - - - +
75I TYR* 2.7 57.3 + - + +
107I GLY* 3.8 21.1 - - - +
109I TYR* 3.6 44.2 - - + +
316I LEU* 4.5 9.0 - - + -
317I ASP* 1.3 82.7 + - - +
319I TRP* 1.3 69.3 + - - +
320I GLN* 4.3 9.9 - - - +
327I PHE* 3.9 23.8 - - + -
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Residues in contact with TRP 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I ALA* 3.4 33.0 - - + -
73I ARG* 3.3 37.5 - - - -
74I PHE* 3.6 44.0 - + + -
105I CYS* 4.8 13.7 - - - -
106I GLY* 3.3 4.8 - - - -
107I GLY* 3.0 26.2 + - - +
109I TYR* 4.8 3.8 + - - +
318I LEU* 1.3 77.8 - - - +
320I GLN* 1.3 69.6 + - - +
321I VAL* 3.7 25.1 - - + +
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Residues in contact with GLN 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I THR* 2.6 35.8 + - - +
70I GLN 4.7 0.6 - - - +
71I LYS 4.1 0.2 - - - -
72I ALA* 3.0 24.9 + - - -
73I ARG 3.0 11.6 + - - -
75I TYR* 4.1 15.3 - - + -
103I ILE* 3.6 23.3 - - + +
105I CYS 3.9 2.7 - - - -
106I GLY* 3.9 0.9 - - - -
107I GLY 3.1 24.0 + - - -
318I LEU* 4.3 5.7 - - + +
319I TRP* 1.3 83.4 - - - +
321I VAL* 1.3 62.6 + - - +
322I LYS 3.7 6.7 - - - +
323I SER* 3.6 9.6 - - - -
325I THR* 2.9 30.8 + - - +
327I 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