Contacts of the strand formed by residues 313 - 317 (chain A) in PDB entry 1UU1
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 GLY 313 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PHE* 3.6 9.0 - - - -
286A VAL 3.1 10.3 - - - -
288A MET* 3.8 9.1 + - - -
293A LYS* 3.8 11.4 - - - +
309A SER* 3.7 0.5 - - - -
310A PHE* 2.8 35.4 + - - +
311A ARG 3.5 0.4 + - - -
312A GLU* 1.3 79.8 - - - +
314A VAL* 1.3 66.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A VAL 3.8 0.5 - - - +
285A PHE* 3.3 5.3 - - - -
286A VAL* 2.7 65.4 + - + +
288A MET* 4.3 14.4 - - - -
293A LYS* 3.9 22.2 - - + -
296A LEU* 5.2 6.1 - - + -
297A LEU* 4.0 18.2 - - + -
307A VAL* 4.1 12.6 - - + -
308A ARG 3.2 11.4 - - - +
309A SER* 4.4 2.5 - - - -
313A GLY* 1.3 79.7 - - - +
315A ARG* 1.3 60.1 + - - +
316A ILE* 3.9 14.3 + - + -
331A LEU* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU 3.8 3.3 - - - +
25A ALA 2.9 29.3 + - - -
26A LEU* 4.3 2.0 - - - +
27A ASN* 3.2 35.9 + - - +
149A ASN* 3.1 21.2 + - - +
150A PRO* 3.7 14.4 - - - +
283A PHE* 3.4 25.2 - - + -
284A VAL 3.2 4.0 - - - +
285A PHE* 3.9 8.7 - - + -
308A ARG* 2.9 37.3 + - + +
310A PHE* 3.5 28.1 - - + -
313A GLY 4.4 0.2 + - - -
314A VAL* 1.3 72.7 - - - +
316A ILE* 1.3 61.4 + - - +
317A THR* 4.6 1.6 - - - -
1336A HSA 2.7 43.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.9 7.4 - - + -
265A MET* 4.9 4.9 - - + -
269A LEU* 5.9 0.2 - - + -
283A PHE* 3.0 3.8 - - - +
284A VAL* 2.7 52.2 + - + +
286A VAL* 4.0 24.7 - - + -
307A VAL* 3.8 23.8 - - + -
314A VAL* 4.2 13.9 - - + +
315A ARG* 1.3 75.7 - - - +
317A THR* 1.3 71.8 + - - +
318A ILE* 4.9 0.5 - - - +
327A ILE* 4.1 35.7 - - + -
331A LEU* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR 5.7 0.9 - - - +
24A LEU* 2.9 51.2 + - + +
25A ALA 4.1 0.9 - - - -
26A LEU 3.9 0.7 + - - -
27A ASN* 2.7 44.4 + - - -
28A GLU* 3.5 26.9 - - + +
265A MET* 5.7 0.6 - - - +
282A ASN* 3.8 6.1 - - - +
283A PHE* 3.6 7.2 - - - -
315A ARG* 4.0 0.7 + - - -
316A ILE* 1.3 80.5 - - - +
318A ILE* 1.3 69.7 + - - +
319A GLY 3.5 0.3 + - - -
324A ASN* 4.3 2.1 - - - +
----------------------------------------------------------
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