Contacts of the strand formed by residues 46 - 52 (chain A) in PDB entry 3KSS
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 GLN 46 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 4.8 14.1 - - - +
44A ASP* 3.6 14.8 + - - +
45A VAL* 1.3 82.7 - - - +
47A VAL* 1.3 68.2 + - - +
48A ILE* 4.4 20.0 + - + +
94A TYR* 4.0 15.8 - - + -
95A VAL 3.1 16.8 - - - +
96A ILE* 4.6 6.6 - - + +
97A PHE* 4.8 1.1 - - - +
134A THR* 5.8 1.8 + - - +
135A GLY 5.8 0.2 - - - +
673A LEU* 3.6 49.1 + - - +
674A SER* 4.8 2.5 - - - +
675A THR* 4.6 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN* 1.3 79.0 - - - +
48A ILE* 1.3 65.3 + - - +
49A ILE* 4.1 2.3 - - + +
93A VAL 3.5 4.5 - - - +
94A TYR* 3.7 1.2 - - - -
95A VAL* 3.0 32.8 + - + +
97A PHE* 4.4 5.8 - - + -
103A PRO 5.4 0.2 - - - +
106A ALA* 4.1 5.6 - - + +
107A ARG* 3.8 26.5 - - + +
110A VAL* 3.4 39.5 - - + -
129A LEU* 3.6 33.7 - - + -
130A GLY 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN* 4.4 21.8 - - + +
47A VAL* 1.3 80.8 - - - +
49A ILE* 1.3 67.4 + - - +
50A LYS 4.4 6.3 - - - +
92A TYR* 4.7 5.8 - - + -
93A VAL 3.9 2.7 - - - +
94A TYR* 3.9 35.0 - - + -
129A LEU* 3.4 1.6 - - - -
130A GLY* 2.5 38.2 + - - +
131A PRO* 4.4 17.9 - - + -
133A ALA 5.1 7.9 - - - +
615A ALA* 3.6 27.8 - - + +
616A THR* 5.8 3.1 - - - +
673A LEU* 5.6 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 4.1 6.1 - - + +
48A ILE* 1.3 83.2 - - - +
50A LYS* 1.3 59.8 + - - +
51A THR* 3.6 3.5 + - - +
69A LEU* 3.5 24.3 - - + +
73A MET* 4.0 17.3 - - + -
91A SER 3.2 12.8 - - - +
93A VAL* 3.0 38.1 + - + +
95A VAL* 4.6 5.8 - - + -
110A VAL* 3.9 21.1 - - + -
114A LEU* 3.8 31.0 - - + -
127A ALA* 4.6 4.9 - - + -
128A GLU 3.1 10.3 - - - +
129A LEU* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.9 2.8 - - - +
49A ILE* 1.3 73.6 - - - +
51A THR* 1.3 65.8 + - - +
52A SER* 4.5 13.9 - - - +
90A ASP* 4.6 8.1 - - - +
92A TYR* 3.2 48.7 - - + +
128A GLU* 2.7 72.9 + - + +
611A LYS* 5.8 2.0 - - - -
613A GLU* 5.3 10.4 + - - +
614A THR* 4.4 8.4 - - - +
615A ALA* 3.8 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS* 1.3 81.3 + - - +
52A SER* 1.3 64.1 + - - +
53A TYR* 5.3 0.5 - - - +
65A VAL* 3.3 30.7 - - + -
69A LEU* 3.3 24.6 - - - +
90A ASP* 3.6 2.8 - - - +
91A SER* 2.8 42.1 + - - -
121A LEU* 4.6 3.8 - - + -
125A VAL* 3.7 18.8 - - + -
126A SER 3.6 17.5 - - - +
127A ALA* 3.9 7.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS* 4.3 17.7 - - - +
51A THR* 1.3 73.6 - - - +
53A TYR* 1.3 68.5 + - - +
54A PRO* 4.6 2.5 - - - +
89A GLY 4.0 2.2 - - - -
90A ASP* 4.2 15.0 + - - -
125A VAL* 3.6 27.4 - - - +
126A SER 4.3 5.0 + - - -
128A GLU* 6.0 0.7 - - - -
273A ARG* 6.1 1.4 - - - -
----------------------------------------------------------
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