Contacts of the strand formed by residues 1029 - 1035 (chain A) in PDB entry 3KHF
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 LYS1029 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952A VAL* 5.1 11.2 - - + -
953A ILE 3.2 9.2 - - - +
954A HIS* 4.7 16.4 - - + +
1007A ASN* 4.6 3.8 + - - +
1026A SER* 4.5 1.4 - - - -
1027A GLY* 3.1 16.6 + - - +
1028A ASN* 1.3 84.3 - - + +
1030A ILE* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1030 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951A ILE 3.5 1.2 - - - +
952A VAL* 3.3 6.2 - - - +
953A ILE* 2.9 57.7 + - + -
960A TYR* 3.9 24.0 - - + +
962A PHE* 6.0 0.2 - - + -
1006A ILE* 3.7 11.4 - - + -
1007A ASN* 3.6 17.9 - - - +
1023A LEU* 3.3 34.5 - - + -
1026A SER* 3.6 20.4 - - - +
1029A LYS* 1.3 75.8 - - - +
1031A SER* 1.3 62.7 + - - +
1032A LEU* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1031 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950A PRO* 3.1 30.5 - - - +
951A ILE 3.3 4.5 - - - -
952A VAL* 4.1 11.3 - - - +
1005A HIS 3.8 0.3 - - - +
1006A ILE* 3.5 4.5 - - - -
1007A ASN* 2.8 49.2 + - - -
1008A GLY 4.6 1.8 + - - -
1030A ILE* 1.3 72.3 - - - +
1032A LEU* 1.3 62.5 + - - +
1033A ARG 4.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1032 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950A PRO* 3.5 1.7 - - - +
951A ILE* 2.8 47.4 + - + +
953A ILE* 3.9 24.5 - - + -
962A PHE* 4.3 12.3 - - + -
997A LEU* 4.0 25.6 - - + -
1003A ILE* 4.3 12.6 - - + -
1005A HIS 3.4 2.9 - - - +
1006A ILE* 3.8 28.3 - - + -
1023A LEU* 4.5 5.2 - - + -
1030A ILE* 3.9 25.1 - - + -
1031A SER* 1.3 77.7 - - - +
1033A ARG* 1.3 62.3 + - - +
1034A THR* 3.9 12.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1033 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A ARG 4.9 10.8 + - - +
949A PRO 5.6 0.7 - - - -
950A PRO* 4.1 23.6 - - + -
1003A ILE* 3.5 1.7 - - - +
1004A THR* 2.9 40.2 + - - +
1005A HIS* 3.0 59.3 + - + +
1008A GLY* 5.9 2.9 - - - +
1031A SER* 4.2 0.6 - - - +
1032A LEU* 1.3 72.8 - - - +
1034A THR* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1034 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A ARG* 5.2 9.5 - - - +
949A PRO 5.9 0.2 + - - -
951A ILE* 3.9 12.6 - - + +
997A LEU* 3.9 27.1 - - + -
1001A ASP* 3.7 22.2 + - + -
1002A LEU 3.0 13.2 - - - +
1003A ILE* 4.3 7.6 - - + -
1004A THR* 4.6 2.2 - - - +
1032A LEU* 3.9 15.6 + - + +
1033A ARG* 1.3 81.4 - - - +
1035A THR* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1035 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000A GLY 4.2 0.5 - - - +
1001A ASP* 4.5 1.6 - - - -
1002A LEU* 2.8 59.7 + - + +
1004A THR* 4.1 10.5 - - + -
1034A THR* 1.3 78.0 - - - +
1036A ALA* 1.3 60.4 + - - +
968B ARG* 2.7 50.6 + - + +
977B TYR* 5.3 2.0 - - + -
----------------------------------------------------------
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