Contacts of the strand formed by residues 281 - 290 (chain A) in PDB entry 4KIS
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 281 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASN* 5.3 7.6 + - - -
272A VAL* 2.7 43.0 + - + +
273A VAL 4.4 1.1 - - - -
274A CYS* 3.5 25.8 - - + -
280A GLY* 1.3 76.7 - - - -
282A VAL* 1.3 66.9 + - - +
300A TYR* 3.0 38.6 - - + -
301A SER 3.3 5.2 - - - -
302A CYS* 3.2 32.8 - - + -
303A LYS* 5.7 0.2 - - - -
316A ASN* 3.9 4.9 - - - -
317A LYS 3.5 20.6 - - - -
319A TRP* 4.6 5.8 - + - -
324A LEU* 5.4 0.7 - - + -
442A ILE* 3.4 32.5 - - + -
15F A 5.7 0.7 - - - +
16F G 4.4 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 1.3 77.6 - - - +
283A HIS* 1.3 78.4 + - - +
284A ARG* 3.7 5.5 + - + +
300A TYR* 3.3 7.6 - - - -
301A SER* 2.9 31.6 + - - +
303A LYS* 3.5 40.4 - - + -
306A LYS* 4.1 31.2 - - + +
307A HIS* 5.4 0.4 - - + -
15F A 4.0 31.0 - - + +
16F G 3.8 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A SER* 3.4 25.0 - - - -
282A VAL* 1.3 88.8 - - - +
284A ARG* 1.3 73.8 + - - +
285A ARG* 4.0 3.5 + - - -
298A ARG* 3.3 39.3 + - + +
299A TYR 3.6 8.7 - - - -
300A TYR* 3.6 29.4 - + + -
16F G 3.1 37.6 + - - +
17F G 2.9 41.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A VAL* 4.3 6.3 - - + +
283A HIS* 1.3 88.5 + - - +
285A ARG* 1.3 65.9 + - - +
286A LYS* 4.6 17.4 - - - +
298A ARG* 3.4 4.0 - - - -
299A TYR* 2.9 50.3 + - + +
301A SER* 2.7 41.4 + - - +
305A TYR* 2.9 27.8 + - - +
306A LYS* 3.4 38.5 - - - +
29E A 6.2 1.0 - - - +
30E G 5.5 4.2 + - - -
31E T 6.3 1.0 - - - +
16F G 5.5 0.4 - - - -
17F G 4.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A HIS* 4.0 2.9 - - + -
284A ARG* 1.3 79.6 + - - +
286A LYS* 1.3 79.0 + - - +
287A ASP* 4.8 8.5 - - - +
296A HIS* 5.4 9.5 - - + +
297A TYR 3.2 14.6 - - - +
298A ARG* 3.2 36.6 - - + +
299A TYR* 5.5 0.9 - - - -
17F G 3.2 42.9 + - + +
18F A 3.3 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ARG* 4.6 17.9 - - - +
285A ARG* 1.3 82.9 - - - +
287A ASP* 1.3 66.8 + - - +
296A HIS* 3.7 0.7 - - - -
297A TYR* 2.9 39.0 + - + +
299A TYR* 4.5 19.7 - - + +
28E T 5.6 3.6 - - + -
29E A 4.0 34.9 - - + +
30E G 2.9 47.4 + - - +
31E T 4.1 5.4 - - - +
18F A 5.9 2.0 - - - +
19F A 3.8 15.7 - - - +
20F C 4.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ARG* 4.8 8.5 - - - +
286A LYS* 1.3 82.3 + - - +
288A THR* 1.3 66.1 + - - +
295A TYR 2.8 19.3 - - - +
296A HIS* 3.4 26.6 + - + +
297A TYR* 5.4 0.4 - - - -
18F A 4.3 30.5 + - - +
19F A 4.4 14.4 + - - +
20F C 4.0 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASP* 1.3 75.8 + - - +
289A VAL* 1.3 81.3 + - - +
295A TYR* 2.6 44.7 + - - +
297A TYR* 5.9 1.2 - - - -
27E T 5.4 7.9 - - + +
28E T 4.6 6.5 - - - -
29E A 3.1 15.8 + - - -
20F C 4.1 1.9 + - - -
21F T 2.5 51.1 + - + +
22F A 4.2 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR* 1.3 91.9 - - - +
290A SER* 1.3 66.6 + - - +
291A ARG 3.5 19.7 - - - +
292A GLY* 3.6 7.9 - - - +
293A LYS 2.8 27.6 - - - +
294A LYS* 3.1 37.2 - - + -
295A TYR* 4.5 2.2 - - - -
27E T 6.4 0.2 - - - -
21F T 4.9 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A VAL* 1.3 75.7 - - - +
291A ARG* 1.3 91.2 + - - +
292A GLY 3.2 0.9 + - - -
293A LYS* 3.1 19.3 + - - +
295A TYR* 4.0 8.0 - - - -
25E G 4.7 0.7 + - - -
26E T 3.4 33.4 - - - +
27E T 5.8 1.1 - - - -
----------------------------------------------------------
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