Contacts of the strand formed by residues 259 - 267 (chain C) in PDB entry 5YGP
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 259 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLU 4.5 0.5 - - - +
113C ALA* 5.1 1.2 - - - -
114C LEU 5.6 0.2 + - - -
156C TYR* 3.5 28.8 + - + -
159C TRP* 3.1 47.9 - + + +
160C PRO* 5.0 1.6 - - - +
168C TYR* 5.4 0.9 - - - -
169C ALA* 3.9 23.8 - - + -
257C LYS 3.7 1.6 + - - -
258C PRO* 1.3 73.6 - - - +
260C VAL* 1.3 63.1 + - - +
261C GLY 3.5 1.9 + - - -
329C GLU* 3.5 28.5 - - + -
330C ILE 4.3 10.1 - - - -
331C MET* 3.5 26.0 - - + -
332C PRO* 4.3 11.7 - - + -
337C MET* 5.2 1.6 - - + -
340C PHE* 3.7 17.3 - + - -
341C TRP* 3.9 20.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C HIS* 3.4 0.3 - - - -
93C PHE* 5.8 2.9 - - + -
111C VAL* 3.7 24.5 - - + -
112C GLU 3.5 13.2 - - - +
113C ALA* 4.6 2.9 - - + -
258C PRO 3.9 7.6 - - - +
259C PHE* 1.3 70.9 - - - +
261C GLY* 1.3 62.2 + - - +
262C VAL* 4.8 0.9 - - + -
325C ALA* 3.5 40.4 - - + +
329C GLU 2.7 23.9 + - - +
330C ILE* 3.4 25.9 - - + +
331C MET* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 4.4 6.7 - - - -
110C ALA 3.7 0.2 - - - +
111C VAL* 3.4 0.9 - - - -
112C GLU* 2.5 52.2 + - - +
156C TYR* 4.6 4.1 + - - -
259C PHE 3.5 3.8 + - - -
260C VAL* 1.3 73.2 - - - +
262C VAL* 1.3 60.7 + - - -
263C LEU 3.8 0.4 - - - -
331C MET* 3.5 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 4.2 1.6 - - - -
65C HIS* 3.0 29.7 + - + +
93C PHE* 5.1 3.4 - - + +
94C THR* 4.5 10.8 - - - +
97C ALA* 3.8 25.4 - - + -
108C PRO* 3.9 22.9 - - + -
109C ILE 4.6 0.2 - - - +
110C ALA 3.3 10.1 - - - +
111C VAL* 4.0 19.3 - - + -
260C VAL* 4.8 1.6 - - + -
261C GLY* 1.3 72.7 - - - -
263C LEU* 1.3 68.2 + - - +
264C SER* 2.8 21.3 + - - +
304C ALA* 6.0 0.2 - - + -
330C ILE* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 5.3 4.5 - - + -
16C LYS* 4.5 20.4 - - + -
62C PHE* 4.5 17.7 - - + -
63C TRP* 3.9 25.6 - - - +
64C ALA* 4.3 3.8 - - - +
108C PRO* 3.5 0.9 - - - +
109C ILE* 2.5 47.6 + - + -
110C ALA* 2.6 20.8 + - + +
112C GLU* 3.5 26.3 + - - +
261C GLY 3.8 2.6 + - - -
262C VAL* 1.3 71.0 - - - +
264C SER* 1.3 61.5 + - - +
300C LEU* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ILE 3.6 0.7 - - - +
62C PHE* 3.3 7.6 - - - -
63C TRP 2.9 34.9 + - - +
65C HIS* 3.9 5.7 - - - +
68C PHE* 3.8 8.0 - - - -
98C VAL* 3.2 30.8 - - - +
106C ALA* 3.8 8.3 - - - -
107C TYR 3.2 11.0 - - - -
108C PRO* 4.1 0.3 - - - +
109C ILE* 4.1 4.9 - - - -
262C VAL* 2.8 18.2 + - - +
263C LEU* 1.3 74.2 + - - +
265C ALA* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 3.8 8.1 - - + -
61C ILE 3.3 5.4 - - - -
62C PHE* 3.5 32.3 - - + -
80C ILE* 5.2 0.5 - - - +
106C ALA* 3.3 3.4 - - - -
107C TYR* 2.8 43.8 + - + +
109C ILE* 4.6 1.6 - - + -
264C SER* 1.3 74.4 - - - +
266C GLY* 1.3 59.7 + - - +
267C ILE* 5.2 0.2 - - - +
281C LEU* 3.8 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 3.2 7.1 - - - +
61C ILE* 3.0 41.6 + - - +
68C PHE* 3.4 21.1 - - - -
77C LEU* 4.9 3.8 - - - -
105C ILE 4.1 10.8 - - - -
106C ALA* 4.3 0.7 - - - -
265C ALA* 1.3 73.3 - - - +
267C ILE* 1.3 63.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASP 3.5 8.7 - - - +
60C ILE* 4.6 0.9 - - + -
77C LEU* 3.5 8.4 - - - +
78C ALA* 2.8 37.9 + - + -
80C ILE* 3.7 26.8 - - + +
105C ILE 4.9 2.6 + - - -
107C TYR* 4.4 4.0 - - + -
265C ALA 5.2 0.2 - - - +
266C GLY* 1.3 75.7 - - - +
268C ASN* 1.3 70.6 + - - +
271C SER* 5.1 2.5 - - - -
274C LYS* 4.1 29.8 - - + +
277C ALA* 3.7 28.3 - - + -
278C LYS* 4.1 13.7 - - + +
281C LEU* 4.2 16.8 - - + -
----------------------------------------------------------
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