Contacts of the strand formed by residues 40 - 46 (chain 1) in PDB entry 1K2I
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 40 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321 SER* 2.7 27.6 + - - +
331 LEU 3.6 4.9 - - - -
341 GLN* 3.7 5.2 - - + -
381 GLY 3.6 4.6 + - - +
391 PHE* 1.3 90.6 - - - +
411 PHE* 1.3 60.8 + - - +
421 CYS 3.1 29.2 + - - -
431 GLY* 4.2 2.0 - - - -
731 GLN* 3.5 26.0 + - - +
1411 TRP* 3.8 41.0 - + + +
1511 THR* 4.7 15.6 + - + +
1931 GLY* 2.9 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331 LEU* 3.0 25.1 + - + -
341 GLN 3.6 7.0 - - - -
351 ASP* 3.6 26.0 - - + -
391 PHE* 3.7 26.7 - - + -
401 HIS* 1.3 79.5 - - - +
421 CYS* 1.3 87.5 + - + +
581 CYS 3.5 25.1 - - - -
591 GLY 5.0 1.1 - - - -
601 VAL* 4.2 11.9 - - + -
641 ASP* 3.5 30.7 - - + -
1931 GLY* 4.1 13.5 - - - -
4001 SN1 4.7 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 42 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331 LEU* 2.7 44.0 + - + -
401 HIS* 3.1 14.3 + - - -
411 PHE* 1.3 101.0 - - + +
431 GLY* 1.3 56.8 + - - +
571 HIS* 5.2 0.9 - - - -
581 CYS* 2.0 55.4 - - + -
1931 GLY 4.0 4.9 - - - -
1951 SER* 3.5 15.7 - - - -
4001 SN1 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301 GLN* 3.9 9.9 - - - -
311 VAL 3.5 11.2 - - - -
331 LEU* 3.7 6.0 - - - +
401 HIS* 4.4 4.3 - - - -
421 CYS* 1.3 75.9 - - - +
441 GLY* 1.3 58.8 + - - -
541 THR* 2.9 21.5 + - - -
1401 GLY* 6.3 0.9 - - - -
1931 GLY 4.1 4.0 + - - -
1941 ASP 4.7 1.8 - - - -
1951 SER 2.7 12.5 + - - -
1961 GLY* 3.3 10.1 - - - -
1971 GLY* 3.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 44 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291 TRP 3.6 0.9 - - - +
301 GLN* 3.6 9.6 + - - +
311 VAL* 3.0 40.7 + - - +
331 LEU* 5.2 0.7 - - - -
431 GLY* 1.3 73.9 - - - -
451 SER* 1.3 65.2 + - - -
521 VAL* 4.3 4.0 - - - -
531 VAL 3.4 12.3 - - - -
541 THR* 4.3 1.6 - - - -
1961 GLY 3.4 6.6 + - - -
1971 GLY* 4.0 1.0 - - - -
1981 PRO* 4.3 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291 TRP* 3.3 10.1 - - - -
311 VAL* 5.0 0.4 - - - -
441 GLY* 1.3 76.7 + - - -
461 LEU* 1.3 63.1 + - - +
471 ILE 3.5 0.3 + - - -
521 VAL* 3.4 5.7 - - - +
531 VAL* 2.8 55.0 + - - +
1211 VAL* 4.2 18.4 - - - -
1961 GLY 4.9 0.7 + - - -
1971 GLY 4.4 0.5 - - - -
1981 PRO* 3.1 33.8 - - - +
2091 LEU* 4.0 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281 PRO 4.2 6.5 - - - +
291 TRP* 2.9 13.0 + - - +
311 VAL* 3.8 24.5 - - + -
451 SER* 1.3 70.8 - - - +
471 ILE* 1.3 60.2 + - - +
481 ASN 3.7 19.7 - - - +
511 TRP 3.7 3.4 - - - +
521 VAL* 3.6 22.2 - - + +
681 ALA* 4.3 5.2 - - + -
831 LEU* 5.3 2.0 - - + -
1081 LEU* 4.4 13.0 - - + -
1121 ALA* 4.4 9.0 - - + -
1141 PHE* 4.4 4.9 - - + -
1181 VAL* 3.7 29.8 - - + -
1191 SER 3.9 16.4 - - - +
1201 ALA* 3.4 2.3 - - - -
1211 VAL* 3.1 28.4 + - - +
----------------------------------------------------------
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