Contacts of the strand formed by residues 311 - 320 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G PHE* 3.4 11.0 - - + -
83G PRO* 3.0 24.4 - - - +
84G PHE* 2.7 52.7 + + + +
85G SER* 4.7 0.2 - - - -
86G ASN* 3.5 30.3 - - + -
91G LEU* 3.9 10.5 - - + -
112G LEU* 3.8 31.6 - - + -
113G PHE 3.6 3.6 - - - +
129G ASN* 3.4 31.4 - - + -
130G ILE* 3.9 13.9 - - + -
308G TYR* 3.6 26.5 - + + -
310G ASN* 1.3 76.5 - - - +
312G GLY* 1.3 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 312 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G SER* 3.3 5.7 - - - -
81G PHE* 3.0 43.1 + - - +
83G PRO* 4.4 0.2 - - - -
113G PHE 2.9 8.0 + - - -
115G ASN* 3.7 25.6 - - - +
310G ASN* 3.5 2.6 + - - -
311G PHE* 1.3 73.7 - - - +
313G VAL* 1.3 66.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G SER* 3.6 28.5 - - - -
79G ALA 3.3 11.9 - - - +
80G SER* 4.0 13.7 - - - +
81G PHE* 3.6 7.1 - - - -
111G LYS 3.7 0.5 - - - +
112G LEU* 3.5 2.9 - - - -
113G PHE* 2.7 45.2 + - + +
114G PRO 4.6 7.0 - - - +
115G ASN* 4.7 6.5 - - - +
117G LEU* 4.1 12.1 - - + +
119G GLN* 4.1 14.4 - - + +
122G MET* 4.0 12.6 - - + -
312G GLY* 1.3 86.6 - - - +
314G LEU* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G PHE* 4.7 13.2 - - + -
37G TRP* 4.1 13.9 - - + -
78G SER* 3.4 1.4 - - - -
79G ALA* 2.9 38.6 + - + +
81G PHE* 3.5 12.3 - - + -
93G VAL* 5.0 3.4 - - + -
95G PHE* 6.1 0.2 - - + -
110G VAL* 4.1 19.5 - - + -
111G LYS 3.3 9.0 - - - +
112G LEU* 4.1 10.3 - - + +
313G VAL* 1.3 75.3 - - - +
315G GLY* 1.3 66.4 + - - +
316G LEU* 4.7 0.9 - - + +
330G PHE* 4.0 36.6 - - + -
332G ILE* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 315 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G LEU 3.6 7.0 - - - -
78G SER* 4.0 9.0 - - - -
110G VAL* 3.6 6.2 - - - +
111G LYS* 2.8 39.5 + - - +
113G PHE* 4.1 4.6 - - - -
122G MET* 4.0 12.6 - - - -
314G LEU* 1.3 77.1 - - - +
316G LEU* 1.3 65.9 + - - -
317G ASP* 3.7 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G TRP* 4.1 11.7 - - + -
49G PHE* 3.9 32.1 - - + -
66G LEU* 3.7 30.5 - - + -
75G TYR 3.8 1.1 - - - -
76G ALA* 3.3 6.1 + - - -
77G LEU* 2.8 35.3 + - + +
109G TYR 4.2 8.5 - - - +
110G VAL* 3.8 28.3 - - + -
122G MET* 4.9 0.4 - - - +
314G LEU* 4.8 0.7 - - + -
315G GLY* 1.3 70.9 - - - -
317G ASP* 1.3 58.5 + - - +
318G LEU* 4.1 7.6 - - + -
327G PHE* 4.1 22.2 - - + -
330G PHE* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 317 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G PHE* 5.4 1.6 - - - -
75G TYR 3.3 12.1 - - - +
76G ALA* 3.9 6.6 - - - +
109G TYR* 3.5 19.1 + - - -
111G LYS* 3.5 33.6 + - + +
113G PHE* 5.3 0.4 - - - -
122G MET* 4.2 19.3 - - + -
123G HIS* 3.2 37.8 - - - +
124G GLY* 3.2 15.5 + - - -
315G GLY 3.7 2.9 + - - -
316G LEU* 1.3 75.7 - - - +
318G LEU* 1.3 65.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 318 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G PHE* 5.2 1.1 - - + -
68G THR* 4.7 5.2 - - + -
74G PHE* 3.3 10.0 - - - -
75G TYR* 2.8 53.8 + - + +
107G GLY* 3.8 20.9 - - - +
109G TYR* 3.6 43.7 - - + +
316G LEU* 4.5 10.1 - - + -
317G ASP* 1.3 81.7 + - - +
319G TRP* 1.3 61.6 + - - +
320G GLN* 3.9 20.4 - - + +
327G PHE* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 319 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G ALA* 3.4 32.3 - - + -
73G ARG* 3.3 38.8 - - - -
74G PHE* 3.6 42.2 - + + -
105G CYS* 4.8 13.8 - - - -
106G GLY* 3.2 4.2 - - - -
107G GLY* 3.0 25.9 + - - +
109G TYR* 4.8 3.6 + - - +
318G LEU* 1.3 75.4 - - - +
320G GLN* 1.3 70.5 + - - +
321G VAL* 3.7 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 320 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G THR* 2.5 35.0 + - - +
70G GLN 5.2 0.4 - - - +
72G ALA* 3.0 5.0 + - - -
73G ARG 3.0 31.9 + - - -
75G TYR* 4.1 12.8 - - + -
103G ILE* 3.8 11.8 - - + +
105G CYS 3.9 4.0 - - - -
106G GLY* 4.1 5.4 - - - -
107G GLY 3.1 20.4 + - - -
318G LEU* 3.9 11.3 - - + +
319G TRP* 1.3 88.4 - - - +
321G VAL* 1.3 66.6 + - - +
322G LYS 4.4 2.5 - - - +
323G SER* 3.6 11.4 - - - -
325G THR* 2.9 30.4 + - - +
327G PHE* 5.0 0.8 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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