Contacts of the strand formed by residues 315 - 320 (chain C) in PDB entry 3UVN
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 ILE 315 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 3.9 1.0 + - - -
53C PHE* 3.8 23.1 - - + -
74C ALA 4.6 6.3 - - - +
75C TYR* 3.9 27.1 - - + -
308C ALA 4.0 0.2 - - - +
309C CYS* 3.7 3.6 - - - +
310C HIS* 2.9 37.9 + - + +
313C GLU* 3.0 32.6 + - + +
314C ASN* 1.3 75.5 - - - +
316C ILE* 1.3 70.6 + - - +
329C LEU* 4.5 10.8 - - + -
330C TRP 3.2 10.5 - - - +
331C LYS* 3.4 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 3.5 40.6 - - + +
267C SER* 5.6 0.2 - - - +
275C VAL* 3.9 30.1 - - + -
283C VAL* 4.6 9.0 - - + -
285C ILE* 3.7 19.5 - - + -
297C LEU* 4.5 3.4 - - + -
307C THR* 4.7 2.9 - - - -
308C ALA 3.4 6.3 - - - +
309C CYS* 4.4 14.4 - - - -
315C ILE* 1.3 80.0 - - - +
317C ALA* 1.3 74.3 + - - +
318C SER* 4.5 1.3 - - - +
329C LEU* 3.4 3.5 - - - -
330C TRP* 2.8 49.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL* 3.9 9.3 - - + +
53C PHE* 3.7 13.3 - - + -
60C LEU* 3.5 42.4 - - + -
307C THR* 3.2 5.4 - - - -
308C ALA* 2.9 31.6 + - + +
316C ILE* 1.3 76.4 - - - +
318C SER* 1.3 58.3 + - - +
327C ILE* 4.6 1.1 - - + -
328C LYS 3.3 6.1 - - - +
329C LEU* 3.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL* 4.5 0.9 - - - -
283C VAL* 3.6 25.8 - - - -
300C HIS* 2.6 27.9 + - - -
304C VAL* 4.0 5.8 - - - -
306C SER 3.3 6.3 - - - -
307C THR* 4.1 2.7 - - - -
316C ILE* 4.7 0.9 - - - -
317C ALA* 1.3 75.6 - - - +
319C ALA* 1.3 59.3 + - - +
327C ILE* 3.1 6.1 - - - +
328C LYS* 2.8 33.4 + - - +
330C TRP* 2.8 22.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C VAL* 3.5 31.2 - - + -
51C VAL* 3.6 18.6 - - + -
300C HIS* 4.2 2.2 - - - -
304C VAL* 3.4 5.9 - - - -
305C ILE* 3.0 25.2 + - + -
306C SER* 2.8 19.8 + - - +
318C SER* 1.3 76.2 - - - +
320C ALA* 1.3 62.1 + - - +
326C THR 3.5 7.6 - - - +
327C ILE* 4.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C VAL* 3.2 23.7 + - - +
300C HIS* 3.4 25.4 - - + +
302C ASP 3.6 10.3 - - - +
303C VAL 3.2 13.9 - - - +
304C VAL* 4.4 0.2 - - - -
305C ILE* 4.5 0.2 - - - -
319C ALA* 1.3 75.4 - - - +
321C LEU* 1.3 70.1 + - - +
324C ASP* 3.4 18.2 - - + -
325C LYS* 3.8 6.7 + - - -
326C THR 3.2 8.5 + - - -
----------------------------------------------------------
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