Contacts of the strand formed by residues 308 - 317 (chain A) in PDB entry 6PI7
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 LEU 308 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR* 1.3 76.0 - - - +
309A GLU* 1.3 65.5 + - - +
310A VAL* 4.7 7.9 - - + -
325A ILE* 5.4 11.0 - - + -
452A VAL* 3.3 3.8 - - - -
453A ALA* 2.7 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 1.3 72.3 - - - +
310A VAL* 1.3 62.8 + - - +
325A ILE* 3.9 5.0 - - - +
326A VAL* 3.0 32.8 + - + +
450A PRO* 4.7 5.3 - - + +
451A LEU 3.2 11.0 - - - +
452A VAL* 4.5 13.7 - - + +
604A UNX 3.3 19.3 - - - -
57C TYR* 3.1 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 4.1 7.6 - - + +
309A GLU* 1.3 79.5 - - - +
311A TYR* 1.4 62.6 + - - +
323A ILE* 3.8 34.1 - - + -
324A GLN 3.2 11.0 - - - +
325A ILE* 4.5 8.3 - - + -
326A VAL* 3.6 8.2 - - - +
450A PRO* 3.5 4.0 - - - +
451A LEU* 2.8 41.7 + - + +
453A ALA* 4.0 30.5 - - + -
471A LEU* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A VAL* 1.4 75.6 - - - +
312A VAL* 1.3 63.1 + - - +
313A SER 3.7 0.2 + - - -
323A ILE* 3.1 7.3 - - - +
324A GLN* 2.9 56.1 + - + +
326A VAL* 3.7 25.4 - - + -
330A SER* 4.3 9.9 - - - -
448A TRP* 3.7 52.6 + + + +
449A LYS 4.0 6.1 - - - -
450A PRO* 4.0 16.4 - - + -
451A LEU* 5.7 0.2 - - - -
55C TYR* 5.0 1.4 + - - -
57C TYR* 3.8 7.6 - + - -
58C TYR* 2.3 44.0 + - - -
104C TYR* 3.9 11.1 - + - -
105C ARG* 4.2 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A VAL* 5.3 0.9 - - + -
311A TYR* 1.3 72.9 - - - +
313A SER* 1.3 51.3 + - - +
314A ALA 3.9 12.3 - - - +
315A SER* 4.8 5.6 - - - -
321A PHE* 4.3 9.9 - - + -
322A TRP 3.4 9.4 - - - +
323A ILE* 4.2 14.6 - - + -
439A PHE* 5.2 1.1 - - + -
443A THR* 3.8 45.1 + - + +
444A HIS 4.3 1.9 + - - +
445A CYS* 3.3 12.1 - - - -
446A ALA* 2.8 30.8 + - - -
448A TRP* 4.8 0.7 + - - -
449A LYS 5.3 0.8 + - - -
451A LEU* 3.9 15.8 - - + +
471A LEU* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A TYR 3.7 1.6 + - - -
312A VAL* 1.3 73.8 - - - +
314A ALA* 1.3 62.0 + - - +
322A TRP* 3.0 18.1 + - - +
324A GLN* 3.8 36.7 - - - +
391A PHE* 2.8 26.0 + - - +
416A ALA* 4.2 1.2 - - - +
445A CYS* 4.3 1.3 - - - -
446A ALA* 3.4 20.7 - - - +
448A TRP* 3.9 15.9 - - - -
108C TYR* 3.9 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A VAL* 3.5 2.5 - - - +
313A SER* 1.3 80.9 + - - +
315A SER* 1.3 58.2 + - - +
321A PHE* 3.6 1.2 - - - +
322A TRP* 2.7 45.6 + - + +
391A PHE 3.5 14.4 - - - +
392A GLY 4.0 6.7 - - - -
393A ASP* 4.2 7.2 - - + +
445A CYS* 3.8 11.4 - - - -
5G ALA* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A VAL* 4.8 2.2 - - - -
314A ALA* 1.3 78.0 - - - +
316A GLU* 1.3 60.9 + - - +
317A HIS 4.6 1.1 - - - -
320A HIS 4.5 0.4 - - - -
321A PHE* 3.5 22.0 - - - +
322A TRP* 3.9 1.3 - - - -
439A PHE* 4.1 14.6 - - - -
440A ASP* 2.8 31.3 + - - -
445A CYS* 4.1 5.6 - - - -
5G ALA* 4.0 5.8 - - - +
6G ARG* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A SER* 1.3 73.2 - - - +
317A HIS* 1.3 83.7 + - + +
320A HIS* 2.4 55.4 + - - +
322A TRP* 3.8 3.1 - - + -
436A LEU* 3.9 5.0 - - - +
3G GLY* 3.4 27.7 + - - -
4G ARG 3.6 22.0 - - - +
6G ARG* 3.4 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A SER* 3.8 0.8 - - - -
316A GLU* 1.3 101.1 + - + +
318A PRO* 1.4 67.1 - - + +
319A ASN* 3.1 41.5 + - + -
320A HIS* 2.7 39.4 + - + +
321A PHE* 3.9 2.9 + - - +
431A TRP* 3.5 19.7 - + + -
436A LEU* 3.4 16.8 - - + -
439A PHE* 4.4 7.6 - - - -
----------------------------------------------------------
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