Contacts of the strand formed by residues 311 - 320 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 3.4 10.3 - - + -
83A PRO* 3.0 24.1 - - - +
84A PHE* 2.8 48.7 + + + +
85A SER* 4.7 0.4 - - - -
86A ASN* 3.4 31.2 - - + -
91A LEU* 3.9 19.5 - - + -
112A LEU* 3.8 31.6 - - + -
113A PHE 3.5 4.0 - - - -
129A ASN* 3.4 31.2 - - + -
130A ILE* 3.9 4.0 - - + -
308A TYR* 3.6 27.6 - + + -
310A ASN* 1.3 77.3 - - - +
312A GLY* 1.3 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER* 3.3 5.9 - - - -
81A PHE* 3.0 42.3 + - - +
83A PRO* 4.4 0.7 - - - -
113A PHE 2.9 6.6 + - - -
115A ASN* 3.7 25.4 - - - +
310A ASN* 3.5 2.6 + - - -
311A PHE* 1.3 74.1 - - - +
313A VAL* 1.3 67.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 3.4 34.1 - - - +
79A ALA 3.3 10.5 - - - +
80A SER* 4.0 14.4 - - - +
81A PHE* 3.6 7.1 - - - -
111A LYS 3.7 0.7 - - - +
112A LEU* 3.5 3.1 - - - -
113A PHE* 2.7 44.4 + - + +
114A PRO 4.6 7.0 - - - +
115A ASN* 4.7 6.5 - - - +
117A LEU* 4.1 12.6 - - + +
119A GLN* 4.1 13.7 - - + +
122A MET* 4.0 10.5 - - + -
312A GLY* 1.3 85.5 - - - +
314A LEU* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 4.7 13.7 - - + -
37A TRP* 4.1 14.7 - - + -
78A SER* 3.3 1.4 - - - -
79A ALA 2.9 39.1 + - - +
81A PHE* 3.5 12.1 - - + -
93A VAL* 5.0 3.4 - - + -
94A GLN 6.2 0.2 - - - +
95A PHE* 6.1 0.2 - - + -
110A VAL* 4.1 20.2 - - + -
111A LYS 3.3 9.2 - - - +
112A LEU* 4.1 10.8 - - + +
313A VAL* 1.3 74.1 - - - +
315A GLY* 1.3 65.6 + - - +
316A LEU* 4.7 0.7 - - + +
330A PHE* 3.9 37.2 - - + -
332A ILE* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU 3.5 7.4 - - - -
78A SER* 3.8 8.5 - - - -
110A VAL* 3.6 7.1 - - - +
111A LYS* 2.8 39.3 + - - +
113A PHE* 4.1 4.4 - - - -
122A MET* 4.0 13.5 - - - -
313A VAL 4.1 1.0 - - - -
314A LEU* 1.3 75.6 - - - +
316A LEU* 1.3 64.8 + - - -
317A ASP* 3.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TRP* 4.1 13.2 - - + -
49A PHE* 3.9 31.8 - - + -
66A LEU* 3.7 29.8 - - + -
75A TYR 3.7 1.1 - - - -
76A ALA* 3.3 6.1 + - - -
77A LEU* 2.8 35.1 + - + +
109A TYR 4.2 9.4 - - - +
110A VAL* 3.8 28.5 - - + -
122A MET* 4.9 0.4 - - - +
314A LEU* 4.4 0.9 + - + -
315A GLY* 1.3 69.6 - - - -
317A ASP* 1.3 59.8 + - - +
318A LEU* 4.1 7.6 - - + -
327A PHE* 4.1 22.2 - - + -
330A PHE* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 6.2 0.5 - - - -
75A TYR 3.3 8.2 - - - +
76A ALA* 4.4 3.9 - - - +
109A TYR* 3.5 19.5 + - - -
111A LYS* 3.5 27.3 + - + +
113A PHE* 5.4 0.7 - - - -
122A MET* 3.5 23.2 - - - +
123A HIS* 3.0 34.8 - - - +
124A GLY* 3.4 19.7 + - - -
315A GLY 3.7 2.6 + - - -
316A LEU* 1.3 74.4 - - - +
318A LEU* 1.3 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 5.2 1.1 - - + -
68A THR* 4.7 5.8 - - + -
73A ARG 4.0 0.2 - - - +
74A PHE* 3.3 9.1 - - - -
75A TYR* 2.7 59.0 + - + +
107A GLY* 3.8 21.3 - - - +
109A TYR* 3.6 44.0 - - + +
316A LEU* 4.5 9.4 - - + -
317A ASP* 1.3 84.6 + - - +
319A TRP* 1.3 67.0 + - - +
320A GLN* 4.3 10.1 - - - +
327A PHE* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 3.5 32.3 - - + -
73A ARG* 3.3 38.6 - - - -
74A PHE* 3.6 43.3 - + + -
105A CYS* 4.8 14.0 - - - -
106A GLY* 3.2 4.4 - - - -
107A GLY 3.0 26.2 + - - +
109A TYR* 4.8 3.2 + - - +
318A LEU* 1.3 77.6 - - - +
320A GLN* 1.3 68.8 + - - +
321A VAL* 3.7 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 2.5 36.4 + - - +
70A GLN 4.7 1.2 - - - +
71A LYS 4.1 0.2 - - - -
72A ALA* 3.0 4.7 + - - -
73A ARG 3.0 32.0 + - - -
75A TYR* 4.1 16.2 - - + +
103A ILE* 3.6 23.2 - - + +
105A CYS 3.9 2.5 - - - -
106A GLY* 3.9 0.4 - - - -
107A GLY 3.1 24.2 + - - -
318A LEU* 4.3 3.7 - - + +
319A TRP* 1.3 80.9 - - - +
321A VAL* 1.3 62.9 + - - +
322A LYS 3.8 6.7 - - - +
323A SER* 3.6 9.9 - - - -
325A THR* 3.0 30.1 + - - +
327A PHE* 5.0 0.6 - - - -
----------------------------------------------------------
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