Contacts of the strand formed by residues 102 - 107 (chain A) in PDB entry 1K63
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 VAL 102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 3.8 10.5 - - + +
33A LEU* 4.0 27.6 - - + -
98A LEU* 3.8 40.2 - - + +
99A GLY 4.0 6.3 - - - +
101A ARG* 1.3 76.5 - - - +
103A VAL* 1.3 74.2 + - - +
104A LEU* 3.8 10.8 + - + -
117A TRP* 4.6 13.0 - - + -
124A ARG 2.9 16.8 + - - +
125A VAL* 3.6 6.4 - - - +
126A GLN 2.9 24.3 + - - +
127A GLY 3.6 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO 3.0 12.4 + - - +
32A ILE* 3.3 18.5 - - + +
33A LEU* 2.8 32.1 + - - +
102A VAL* 1.3 75.3 - - - +
104A LEU* 1.3 64.7 + - - +
105A VAL* 4.3 4.9 - - + -
126A GLN* 3.4 28.0 - - + +
127A GLY 3.4 13.2 - - - +
129A ALA* 5.3 0.7 - - + -
286A ILE* 5.6 0.2 - - + -
289A PHE* 4.5 10.8 - - + -
290A VAL* 4.3 16.8 - - + -
293A LEU* 3.9 19.3 - - + -
294A ARG* 3.8 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.5 33.7 - - + +
35A GLN* 6.4 0.2 - - + -
93A TRP* 4.2 18.8 - - + -
102A VAL* 4.0 9.4 - - + -
103A VAL* 1.3 75.4 - - - +
105A VAL* 1.3 57.4 + - - +
106A VAL* 4.2 13.5 - - + -
114A GLY* 3.8 23.3 - - - +
117A TRP* 4.3 7.4 - - + -
118A ALA* 4.0 17.3 - - + -
125A VAL* 4.0 19.7 - - + -
127A GLY 3.1 9.0 + - - +
128A ILE* 3.5 11.6 - - + -
129A ALA* 2.7 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 3.8 28.0 - - + -
33A LEU 2.8 10.5 + - - +
34A PHE* 3.2 30.8 - - + -
35A GLN 2.8 25.8 + - - -
45A TRP* 3.8 15.2 - - + -
103A VAL* 4.3 3.6 - - + -
104A LEU* 1.3 77.7 - - - +
106A VAL* 1.3 62.6 + - - +
129A ALA* 3.2 13.7 - - + -
131A MET* 3.9 7.6 - - + -
286A ILE* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 5.1 0.4 - - - +
35A GLN* 3.8 11.4 - - + -
45A TRP* 4.0 3.1 - - - -
104A LEU* 4.2 15.5 - - + -
105A VAL* 1.3 86.5 - - - +
107A HIS* 1.3 64.1 + - - +
110A GLY 3.6 15.0 - - - +
111A SER* 3.5 24.5 - - - -
114A GLY* 4.3 11.2 - - - -
115A PHE* 4.0 11.7 - - + -
128A ILE* 4.7 3.1 - - + -
129A ALA 2.9 18.3 + - - +
130A TYR* 3.5 17.2 - - + -
131A MET* 3.2 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLN 3.3 7.4 + - - +
36A HIS* 5.0 0.7 - - - -
37A GLY 3.9 5.6 + - - -
40A THR* 5.2 0.4 + - - -
44A LEU* 3.5 15.6 - - + +
45A TRP* 3.9 9.2 - - + -
106A VAL* 1.3 77.4 - - - +
108A ASP* 1.3 67.1 + - + +
110A GLY* 2.7 29.6 + - - -
111A SER* 3.6 2.5 - - - -
131A MET* 3.3 21.8 - - + +
132A GLU* 3.5 9.8 - - + +
272A HIS* 2.9 47.8 + - - -
273A PHE* 3.7 22.9 - + - -
274A ILE* 5.4 0.2 - - + -
275A GLN* 3.2 30.7 + - - +
----------------------------------------------------------
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