Contacts of the strand formed by residues 311 - 320 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H PHE* 3.4 10.3 - - + -
83H PRO* 3.0 24.4 - - - +
84H PHE* 2.7 53.9 + + + +
85H SER* 4.7 0.4 - - - -
86H ASN* 3.4 30.7 - - + -
91H LEU* 3.9 19.5 - - + -
112H LEU* 3.8 30.1 - - + -
113H PHE 3.6 3.8 - - - -
129H ASN* 3.4 31.6 - - + -
130H ILE* 4.1 5.8 - - + -
308H TYR* 3.6 27.4 - + + -
310H ASN* 1.3 77.2 - - - +
312H GLY* 1.3 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 312 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H SER* 3.2 6.8 - - - -
81H PHE* 2.9 41.3 + - - +
83H PRO* 4.4 0.7 - - - -
113H PHE 2.9 12.3 + - - -
115H ASN* 3.5 25.7 + - - +
310H ASN* 3.5 2.6 + - - -
311H PHE* 1.3 73.5 - - - +
313H VAL* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H SER* 3.4 35.0 - - - +
79H ALA 3.3 10.1 - - - +
80H SER* 4.2 5.8 - - - -
81H PHE* 3.6 8.2 - - - -
111H LYS 3.7 0.3 - - - +
112H LEU* 3.5 3.1 - - - +
113H PHE* 2.7 44.1 + - + +
114H PRO 4.6 7.2 - - - +
115H ASN* 4.7 6.3 - - - +
117H LEU* 4.1 12.1 - - + +
119H GLN* 4.1 21.5 - - + +
122H MET* 3.9 10.5 - - + -
312H GLY* 1.3 85.6 - - - +
314H LEU* 1.3 63.6 + - - +
315H GLY 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H PHE* 4.7 12.3 - - + -
37H TRP* 4.1 9.8 - - + -
78H SER* 3.3 1.4 - - - -
79H ALA* 2.9 38.3 + - + +
81H PHE* 3.5 11.7 - - + -
93H VAL* 5.0 3.4 - - + -
95H PHE* 6.1 0.2 - - + -
110H VAL* 4.1 17.9 - - + -
111H LYS 3.3 8.5 - - - +
112H LEU* 3.9 7.6 - - + -
313H VAL* 1.3 74.5 - - - +
315H GLY* 1.3 62.5 + - - +
316H LEU* 3.7 25.6 - - + -
330H PHE* 4.0 28.3 - - + -
332H ILE* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 315 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H LEU 3.6 7.4 - - - -
78H SER* 3.8 8.5 - - - -
110H VAL* 3.6 2.9 - - - +
111H LYS* 2.8 40.4 + - - +
113H PHE* 4.1 4.9 - - - -
122H MET* 4.0 12.6 - - - -
313H VAL 4.1 1.0 - - - -
314H LEU* 1.3 72.8 - - - +
316H LEU* 1.3 71.2 + - - +
317H ASP 3.7 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H TRP* 4.0 11.7 - - + -
49H PHE* 3.9 32.3 - - + -
66H LEU* 3.6 31.4 - - + -
75H TYR 3.6 0.7 - - - +
76H ALA* 3.3 6.2 + - - -
77H LEU* 2.8 33.9 + - + +
109H TYR 4.6 1.8 - - - +
110H VAL* 4.1 7.9 - - + -
122H MET* 5.1 0.2 - - - -
314H LEU* 3.7 20.9 - - + -
315H GLY* 1.3 77.9 - - - +
317H ASP* 1.3 60.6 + - - +
318H LEU* 4.1 13.0 - - + -
327H PHE* 4.4 15.7 - - + -
330H PHE* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 317 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H PHE* 6.1 0.5 - - - -
75H TYR 3.3 8.2 - - - +
76H ALA* 4.4 4.5 - - - +
109H TYR* 3.5 19.4 + - - -
111H LYS* 3.5 28.3 + - + +
113H PHE* 5.1 0.7 - - + -
122H MET* 3.5 22.7 - - - +
123H HIS* 3.0 35.5 - - - +
124H GLY* 3.4 19.7 + - - -
315H GLY 3.7 2.6 + - - -
316H LEU* 1.3 75.0 - - - +
318H LEU* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 318 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H PHE* 5.2 0.7 - - + -
68H THR* 4.7 5.6 - - + -
73H ARG 4.0 0.3 - - - +
74H PHE* 3.3 9.0 - - - -
75H TYR* 2.8 49.0 + - + +
107H GLY* 3.9 23.6 - - - +
109H TYR* 3.6 41.1 - - + +
316H LEU* 4.5 8.5 - - + -
317H ASP* 1.3 84.5 + - - +
319H TRP* 1.3 60.9 + - - +
320H GLN* 3.9 21.1 - - + +
327H PHE* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 319 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H ALA* 3.5 31.2 - - + -
73H ARG* 3.3 37.7 - - - -
74H PHE* 3.6 44.0 - + + -
105H CYS* 4.8 14.0 - - - -
106H GLY* 3.2 5.0 - - - -
107H GLY 3.0 25.9 + - - +
109H TYR* 4.8 3.6 + - - +
318H LEU* 1.3 75.6 - - - +
320H GLN* 1.3 73.1 + - - +
321H VAL* 3.7 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 320 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H THR* 2.5 37.3 + - + +
70H GLN 4.7 1.1 - - - +
72H ALA* 3.0 5.5 + - - -
73H ARG 3.0 31.7 + - - -
75H TYR* 4.2 12.3 - - + -
103H ILE* 3.8 12.8 - - + +
105H CYS 3.9 4.3 - - - -
106H GLY* 4.1 6.1 - - - -
107H GLY 3.1 20.8 + - - -
318H LEU* 3.9 11.0 - - + +
319H TRP* 1.3 88.2 - - - +
321H VAL* 1.3 64.0 + - - +
322H LYS 3.9 4.0 - - - +
323H SER* 3.6 11.5 - - - -
325H THR* 2.9 29.0 + - - +
327H 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