Contacts of the strand formed by residues 129 - 134 (chain A) in PDB entry 5KJH
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 LYS 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TYR* 3.4 6.1 - - - +
124A ASN* 2.7 53.7 + - + +
127A GLU* 3.5 35.8 + - + +
128A GLY* 1.3 78.0 - - - +
130A LEU* 1.3 62.0 + - - +
293B ILE* 3.9 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 4.2 8.7 - - + -
122A VAL 3.7 20.2 - - - +
123A TYR* 3.9 21.5 - - + -
129A LYS* 1.3 75.2 - - - +
131A TYR* 1.3 64.1 + - - +
132A ARG* 3.8 16.4 - - - +
133A THR* 3.8 11.7 - - - +
293B ILE* 3.8 17.2 - - + +
294B LYS 4.1 10.5 - - - +
295B PRO* 4.4 3.1 - - + -
296B ASP* 3.4 44.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP* 3.3 27.1 + - - -
104A PRO* 3.5 25.7 - - + +
105A ILE* 6.0 0.2 - - - +
110A LEU* 3.8 41.7 - - + -
122A VAL* 2.7 21.4 + - + +
124A ASN* 4.2 12.3 - - + +
129A LYS 3.6 2.2 + - - -
130A LEU* 1.3 74.5 - - - +
132A ARG* 1.3 91.8 + - + +
168A LEU* 4.6 7.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 2.8 44.2 + - + +
130A LEU* 3.6 7.8 - - - +
131A TYR* 1.3 109.6 + - + +
133A THR* 1.3 65.1 + - - +
134A LEU* 3.9 15.5 - - + +
167A SER 4.5 2.8 + - - -
168A LEU* 3.7 35.8 + - + +
169A ALA 5.1 0.2 + - - -
173A GLU* 2.8 51.0 + - - +
176A PRO* 3.7 19.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASN* 3.8 28.3 - - + +
120A VAL 3.2 11.7 - - - +
121A LYS* 4.4 9.8 - - + +
130A LEU* 3.8 12.5 - - - +
132A ARG* 1.3 81.8 + - - +
134A LEU* 1.3 68.8 + - - +
135A VAL* 3.9 14.1 + - + -
176A PRO* 5.9 0.5 - - - +
295B PRO* 5.6 1.9 - - + +
296B ASP* 3.5 19.3 + - - -
297B ARG* 4.3 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLY 4.5 1.0 - - - +
119A ASN* 3.4 6.9 - - - +
120A VAL* 2.8 66.7 + - + +
122A VAL* 4.2 12.8 - - + -
132A ARG* 3.9 20.6 - - - +
133A THR* 1.3 71.1 - - - +
135A VAL* 1.3 60.0 + - - +
141A ILE* 5.5 0.2 - - - +
154A ILE* 5.1 7.6 - - + -
166A TRP* 3.9 44.8 - - + -
168A LEU* 4.1 15.9 - - + -
176A PRO* 3.8 32.3 - - + -
----------------------------------------------------------
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