Contacts of the strand formed by residues 269 - 277 (chain A) in PDB entry 1K30
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 269 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASN* 3.3 12.6 - - - -
262A ILE* 3.6 31.6 - - - +
267A VAL 3.3 3.0 + - - -
268A PRO* 1.3 74.2 - - - +
270A HIS* 1.3 69.8 + - - -
271A LEU* 5.2 1.1 - - - -
310A GLU* 4.4 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LYS* 3.4 32.1 - - + +
131A HIS* 2.8 40.3 + + + +
132A ASN 3.0 17.7 + - - +
133A VAL* 3.4 4.1 - - + +
134A VAL* 2.8 26.9 + - - +
262A ILE* 4.6 0.8 - - - +
268A PRO* 5.2 2.0 - - + -
269A GLY* 1.3 83.3 + - - -
271A LEU* 1.3 66.0 + - - +
272A PHE* 3.6 19.1 - - + -
310A GLU* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 3.2 11.4 - - + -
136A ILE* 3.9 30.1 - - + -
255A VAL* 4.5 6.3 - - + +
258A MET* 5.3 1.6 - - + -
259A ARG* 4.3 20.0 - - + +
262A ILE* 3.3 35.2 - - + -
269A GLY 5.2 0.4 - - - -
270A HIS* 1.3 77.0 - - - +
272A PHE* 1.3 62.5 + - - +
273A PRO* 4.2 1.2 - - - +
310A GLU* 3.1 25.5 + - - +
311A ILE 4.3 2.6 + - - -
330A TYR* 3.2 41.2 + - + +
334A LEU* 4.4 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 5.2 11.0 - - + -
122A ASP* 3.9 18.6 - - - -
123A ILE* 3.8 27.4 - - + -
126A LYS* 4.1 8.5 - - + -
133A VAL* 3.7 21.3 - - + -
134A VAL 2.8 9.7 + - - +
135A LEU* 3.5 8.5 - - + -
136A ILE* 2.7 32.7 + - - -
270A HIS* 3.6 22.0 - - + -
271A LEU* 1.3 78.2 - - - +
273A PRO* 1.3 62.4 - - + +
274A LEU* 3.5 0.9 + - - +
307A VAL* 3.8 20.4 - - + -
308A ALA 3.4 18.2 - - - -
309A PRO* 4.4 4.7 - - + -
310A GLU* 3.9 30.5 - - + -
334A LEU* 4.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE 3.4 7.6 - - - +
271A LEU 4.2 1.3 - - - +
272A PHE* 1.3 82.1 - - - +
274A LEU* 1.3 59.8 + - - +
307A VAL* 3.4 3.9 - - - +
308A ALA 3.2 33.4 + - - +
309A PRO 3.3 15.0 - - - +
310A GLU* 4.3 0.7 - - - -
311A ILE* 5.0 2.2 - - + +
334A LEU* 3.9 31.6 - - + +
337A SER* 3.2 38.1 - - - +
338A VAL* 3.9 3.6 - - + -
341A GLN* 3.1 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PHE* 3.9 20.6 - - + -
135A LEU* 4.3 21.8 - - + -
136A ILE 2.8 12.9 + - - +
137A SER* 3.2 38.2 - - - +
138A ASN 3.5 1.0 + - - -
148A ILE* 4.1 8.7 - - + -
228A TRP* 3.7 23.1 - - + +
272A PHE 3.5 0.6 + - - +
273A PRO* 1.3 76.3 - - - +
275A ALA* 1.3 58.1 + - - +
276A LEU* 4.5 2.5 - - + -
305A LEU* 3.9 19.5 - - + -
306A SER 3.3 21.5 - - - +
307A VAL* 3.8 18.8 - - + -
338A VAL* 3.3 13.8 - - - +
341A GLN* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASN* 3.4 5.2 - - - +
274A LEU* 1.3 73.8 - - - +
276A LEU* 1.3 64.0 + - - +
305A LEU* 3.3 7.1 - - - +
306A SER 2.8 35.1 + - - +
338A VAL* 3.6 24.0 - - + +
341A GLN* 3.7 12.4 + - + -
342A TYR* 3.7 24.0 - - + +
345A LEU* 3.9 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER* 3.8 19.3 - - - +
138A ASN* 2.8 37.7 + - - +
140A GLN* 3.6 7.4 - - + -
144A ASP* 3.8 33.7 - - + +
147A ILE* 4.3 13.5 - - + -
148A ILE* 3.8 15.7 - - + -
228A TRP* 4.0 11.4 - - - +
274A LEU* 4.5 1.3 - - + -
275A ALA* 1.3 74.9 - - - +
277A LEU* 1.3 59.6 + - - +
278A CYS* 4.0 10.1 - - - -
304A GLY 3.4 8.3 - - - +
305A LEU* 3.4 31.4 - - + -
342A TYR* 3.4 9.5 - - - -
345A LEU* 4.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN* 3.5 1.6 - - - -
276A LEU* 1.3 76.0 - - - +
278A CYS* 1.3 65.8 + - - +
279A HIS* 4.4 9.0 - - + +
280A ASP* 4.2 18.2 - - - +
302A GLY 5.0 3.6 - - - +
303A ALA* 3.3 5.2 - - - -
304A GLY* 2.8 39.1 + - - +
342A TYR* 3.7 26.7 - - + +
345A LEU* 3.8 19.7 - - + +
346A LYS* 3.4 47.1 - - + +
349A ILE* 4.6 15.9 - - + -
350A SER* 4.9 4.3 - - - +
----------------------------------------------------------
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