Contacts of the strand formed by residues 126 - 130 (chain P) in PDB entry 3KYM
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 SER 126 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123P LYS* 4.7 8.7 + - - -
125P PRO* 1.3 76.5 - - - +
127P VAL* 1.3 64.7 + - - +
128P PHE* 3.5 31.9 - - - -
147P LEU 4.0 0.2 - - - -
148P VAL* 3.3 6.6 - - - -
149P LYS* 2.7 39.9 + - - +
150P ASP* 4.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123O GLU* 3.7 17.8 - - - +
125P PRO* 4.8 4.3 - - + +
126P SER* 1.3 79.2 - - - +
128P PHE* 1.3 64.8 + - - +
146P CYS* 3.8 6.7 - - + -
147P LEU 3.2 6.3 - - - +
148P VAL* 4.9 2.2 - - + -
202P CYS* 3.6 19.1 - - - -
204P VAL* 4.0 26.0 - - + -
213P VAL* 3.9 34.2 - - + +
215P LYS* 3.6 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121O SER* 3.2 18.6 - - - +
123O GLU* 3.7 24.2 - - + -
124O GLN* 3.6 52.3 - - + +
127O SER* 5.5 4.0 - - - -
126P SER* 3.5 31.9 - - - -
127P VAL* 1.3 79.9 - - - +
129P PRO* 1.4 65.3 - - + +
146P CYS* 3.5 3.1 - - - -
147P LEU* 2.8 54.4 + - + +
149P LYS* 4.1 17.3 - - + -
215P LYS* 4.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 129 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119O PRO 4.9 4.2 - - - +
121O SER* 3.9 25.3 + - - -
123O GLU* 4.0 8.3 - - + +
128P PHE* 1.4 89.7 - - + +
130P LEU* 1.3 64.7 + - - +
131P ALA* 3.8 6.3 + - + +
145P GLY 4.1 5.6 - - - +
146P CYS* 5.0 0.2 - - - -
215P LYS* 3.7 30.3 - - - +
217P VAL* 3.7 30.1 - - + -
218P GLU 5.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O PHE* 3.6 32.8 - - + +
119O PRO 5.3 2.7 - - - +
131O SER 6.1 0.7 - - - +
133O VAL* 3.8 28.5 - - + -
129P PRO* 1.3 75.9 - - - +
131P ALA* 1.3 60.7 + - - +
144P LEU* 3.4 11.8 - - - +
145P GLY* 3.1 41.4 + - - +
146P CYS 3.7 17.9 - - - +
147P LEU* 4.1 17.5 - - + +
185P SER* 3.9 26.0 - - - -
187P VAL* 3.9 9.9 - - + -
217P VAL* 3.7 3.2 - - - +
----------------------------------------------------------
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