Contacts of the helix formed by residues 310 - 322 (chain K) in PDB entry 1UW9
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 HIS 310 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134K ARG* 3.5 32.6 - - - +
135K LEU 2.9 10.6 + - - +
136K GLU* 3.8 16.2 - - - +
302K ASP* 4.3 0.4 - - - -
309K ILE* 1.3 81.8 - - - +
311K PHE* 1.3 82.0 + - + +
312K ARG* 3.0 63.8 + - - +
313K VAL* 3.1 10.7 + - - +
314K LEU* 3.6 2.1 + - - +
341K VAL* 3.4 23.2 - - + +
345K PHE* 4.1 9.2 - + - -
473K ASP* 2.9 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 311 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269K TYR* 4.1 17.5 - - - -
295K ARG* 3.5 35.9 - - + -
298K HIS* 3.9 2.9 - - + -
302K ASP* 3.3 32.0 + - - +
310K HIS* 1.3 80.3 + - + +
312K ARG* 1.3 58.1 + - - +
314K LEU* 2.9 13.2 + - + -
315K ALA* 2.8 39.3 + - + -
326K LEU* 3.8 17.9 - - + -
327K HIS 3.4 22.2 - - - -
328K SER* 4.7 0.2 - - - -
345K PHE* 3.7 37.0 - + - -
349K MET* 4.7 1.1 - - - -
1481K EDO 3.6 16.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 312 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136K GLU* 2.8 63.3 + - - +
137K ASP* 4.0 17.5 - - - +
310K HIS* 3.0 44.7 + - - +
311K PHE* 1.3 76.8 - - - +
313K VAL* 1.3 59.9 + - - +
315K ALA* 3.4 3.4 + - - +
316K LYS* 3.0 32.2 + - - +
341K VAL* 4.4 4.8 + - - +
345K PHE* 3.7 30.6 - - + +
348K LEU* 4.0 15.5 - - + +
360K ARG 4.5 3.8 + - - -
361K GLY* 2.8 43.9 + - - -
362K ILE* 5.4 0.4 - - - +
363K TYR* 4.0 3.8 - - - -
475K LEU* 4.1 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117K PHE* 4.1 12.3 - - + -
135K LEU* 3.9 15.5 - - + +
136K GLU 3.6 9.9 - - - +
137K ASP* 3.5 40.2 - - - +
138K LEU* 3.8 27.3 - - + +
309K ILE* 3.6 23.6 - - + -
310K HIS 3.1 3.7 + - - +
312K ARG* 1.3 75.2 - - + +
314K LEU* 1.3 59.7 + - - +
315K ALA 3.1 0.2 - - - -
316K LYS* 3.3 8.3 + - + +
317K ALA* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E MET* 5.9 0.7 - - + -
117K PHE* 3.9 25.8 - - + -
269K TYR* 2.9 28.6 + - + +
270K LEU* 4.4 17.0 - - + -
274K PHE* 5.4 0.4 - - + -
298K HIS* 4.1 28.0 - - + +
301K ILE* 4.1 26.0 - - + -
302K ASP* 4.1 15.7 - - + +
309K ILE* 3.9 16.4 - - + -
310K HIS 4.0 8.7 - - - +
311K PHE* 2.9 11.5 + - + +
313K VAL* 1.3 76.5 - - - +
315K ALA* 1.3 57.2 + - - +
317K ALA* 3.6 5.4 + - - +
318K LEU* 3.1 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311K PHE* 2.8 26.0 + - + +
312K ARG* 3.6 9.0 - - - +
314K LEU* 1.3 75.4 - - - +
316K LYS* 1.3 60.0 + - + +
318K LEU* 3.3 3.8 + - - +
319K ARG* 2.9 28.8 + - - +
326K LEU* 3.8 26.3 - - + +
345K PHE* 4.9 4.0 - - + +
348K LEU* 6.1 2.2 - - + -
349K MET* 3.9 21.9 - - + +
374K VAL* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 316 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137K ASP* 3.2 21.0 + - - +
138K LEU* 2.6 35.9 + - + +
139K ARG* 4.6 0.6 - - - +
140K ILE* 4.4 12.1 - - + -
312K ARG 3.0 18.8 + - - +
313K VAL* 3.6 8.1 - - + +
315K ALA* 1.3 72.7 - - - +
317K ALA* 1.3 65.7 + - - +
319K ARG* 3.2 3.6 + - - +
320K MET* 3.0 30.4 + - - +
348K LEU* 3.8 35.7 - - + +
364K PHE* 4.9 3.8 + - - +
366K GLN* 2.8 32.2 + - - +
368K TRP* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 317 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K VAL* 3.4 14.6 - - + +
116K MET* 4.9 2.6 - - + +
117K PHE* 3.7 28.3 - - + -
274K PHE* 3.7 19.7 - - + -
313K VAL 2.9 17.2 + - - +
314K LEU 3.7 5.4 - - - +
316K LYS* 1.3 77.1 - - - +
318K LEU* 1.3 57.1 + - - +
320K MET* 3.2 11.1 + - - -
321K SER* 2.8 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 318 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269K TYR* 3.5 36.2 - - + +
277K ASN* 3.7 20.6 - - - +
293K ILE* 3.7 33.0 - - + -
314K LEU 3.1 12.0 + - - +
315K ALA 3.6 4.5 - - - +
317K ALA* 1.3 73.9 - - - +
319K ARG* 1.3 58.7 - - - +
321K SER* 4.4 2.9 - - - -
322K GLY* 2.7 38.0 + - - +
323K GLY* 4.0 12.1 - - - +
326K LEU* 4.0 30.7 - - + -
374K VAL* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 319 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K HYP 2.8 38.9 + - - +
315K ALA 2.9 14.2 + - - +
316K LYS* 3.5 8.5 - - - +
318K LEU* 1.3 76.9 - - - +
320K MET* 1.3 61.0 + - - +
322K GLY 3.8 0.7 + - - -
348K LEU 2.7 35.2 + - - -
349K MET* 3.0 27.5 + - + +
350K ARG 4.0 0.4 + - - -
351K ASP 2.8 31.1 + - - -
352K ASP* 4.6 0.8 - - - +
368K TRP* 3.2 30.8 - - + +
371K MET* 2.8 38.0 + - - +
372K PRO 3.0 18.4 + - - +
373K GLY* 3.6 5.4 - - - +
374K VAL* 3.6 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 320 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K VAL* 3.7 6.7 - - + -
116K MET* 4.0 20.6 - - + -
140K ILE* 3.7 41.3 - - + -
144K TYR* 4.0 8.3 - - + -
145K VAL* 5.7 1.1 - - + -
148K PHE* 3.4 53.4 - - + -
150K GLY* 3.5 18.2 + - - -
278K THR* 5.7 0.3 - - - +
316K LYS 3.0 20.7 + - - +
317K ALA* 3.5 6.5 - - - +
319K ARG* 1.3 74.8 - - - +
321K SER* 1.3 64.5 + - - +
368K TRP* 3.8 16.2 - - + -
371K MET* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 321 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K VAL* 3.7 13.4 - - - +
148K PHE* 5.0 0.9 - - - -
149K VAL* 6.1 0.5 - - - +
150K GLY* 4.2 3.5 + - - +
274K PHE* 3.8 16.7 + - - -
277K ASN* 3.0 19.9 + - - +
278K THR* 2.8 43.7 + - - +
281K ALA* 3.6 13.9 - - - +
282K ILE* 6.0 0.3 - - - +
317K ALA 2.8 18.4 + - - -
318K LEU* 3.8 4.5 - - - -
320K MET* 1.3 74.3 - - - +
322K GLY* 1.3 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 322 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150K GLY 3.6 24.5 - - - -
151K HYP 3.8 1.6 - - - -
152K PRO* 4.1 0.9 - - - -
277K ASN* 3.1 19.8 - - - +
281K ALA* 3.8 15.5 - - - +
291K LEU* 3.8 5.4 - - - +
293K ILE* 4.0 0.5 - - - +
318K LEU* 2.7 21.7 + - - +
320K MET 3.3 1.2 - - - -
321K SER* 1.3 74.6 - - - +
323K GLY* 1.3 57.8 + - - -
----------------------------------------------------------
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