Contacts of the strand formed by residues 139 - 144 (chain K) in PDB entry 6R90
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 LEU 139 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110K ASP* 4.2 18.6 - - - +
112K ILE 6.0 0.9 - - - +
133K LEU 4.7 1.7 - - - +
134K ARG* 4.6 12.1 - - - +
135K LEU 5.1 0.3 + - - -
136K TYR* 3.2 35.6 + - + +
137K ASP 3.2 4.8 - - - +
138K GLY* 1.3 86.5 - - - +
140K PHE* 1.3 59.8 + - - +
141K LYS 4.2 0.2 - - - -
156K ASN* 4.1 32.5 - - + +
157K ILE 3.5 9.2 - - - +
158K ARG* 4.5 5.6 - - + +
159K LEU* 4.2 7.9 - - - +
317L ALA* 5.3 7.4 - - + -
318L SER* 4.1 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123K ILE* 4.8 4.3 - - + -
130K MET* 5.7 0.2 - - - -
132K GLY* 3.5 21.3 - - - -
133K LEU 3.8 22.9 - - - -
134K ARG* 4.8 7.0 - - + -
139K LEU* 1.3 74.5 - - - +
141K LYS* 1.3 62.6 + - - +
142K VAL* 3.6 33.2 + - + -
155K PHE 3.8 0.9 - - - +
156K ASN* 3.5 3.5 - - - -
157K ILE* 2.9 35.4 + - + +
159K LEU* 4.9 10.3 - - + -
167K VAL* 4.7 20.4 - - + -
169K PHE* 4.5 5.4 - + - -
178K ILE* 4.1 27.8 - - + -
195K VAL* 4.9 4.9 - - + -
202K PHE* 3.8 35.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108K VAL* 2.6 53.6 + - + +
109K GLN 4.5 1.0 + - - -
110K ASP* 3.0 25.2 + - - -
131K ILE 3.8 0.3 - - - +
132K GLY* 3.4 4.9 - - - -
133K LEU* 2.9 55.0 + - + +
135K LEU* 4.2 14.1 - - + -
136K TYR* 5.4 0.4 - - - -
139K LEU 4.2 0.8 - - - -
140K PHE* 1.3 74.6 - - - +
142K VAL* 1.3 64.5 + - - +
143K ILE* 4.9 0.4 - - + -
154K ALA* 3.8 23.5 - - + +
155K PHE 3.7 0.9 - - - +
156K ASN* 3.6 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130K MET* 4.0 25.6 - - + -
131K ILE 3.3 8.7 - - - +
140K PHE* 3.6 31.2 - - + +
141K LYS* 1.3 77.8 - - - +
143K ILE* 1.3 63.1 + - - +
144K PRO* 3.5 2.9 - - - +
154K ALA* 3.0 7.5 - - - +
155K PHE* 2.9 68.6 + - + +
157K ILE* 4.0 12.1 - - + -
195K VAL* 4.3 5.2 - - + -
197K LEU* 4.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K PHE* 4.2 21.3 - - + -
86K ALA* 4.3 4.3 - - + -
108K VAL* 3.9 16.6 - - + -
130K MET* 3.5 0.2 - - - -
131K ILE* 2.9 48.4 + - + +
133K LEU* 3.8 29.8 - - + -
141K LYS* 4.9 1.1 - - + -
142K VAL* 1.3 75.4 - - - +
144K PRO* 1.3 67.3 - - - +
145K LEU* 3.4 3.1 + - + +
149K ASN* 3.3 22.9 - - - +
152K LEU* 3.8 24.0 - - + +
153K LYS 3.6 5.6 - - - +
154K ALA* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 144 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129K ARG 4.1 6.1 - - - +
130K MET* 4.3 4.5 - - + -
142K VAL* 3.5 9.8 - - - +
143K ILE* 1.3 83.2 - - - +
145K LEU* 1.3 58.2 + - - +
146K ASP* 3.0 15.1 + - + +
149K ASN* 2.7 30.7 + - - +
153K LYS 3.4 17.5 - - - +
154K ALA* 4.3 2.5 - - - -
155K PHE* 4.1 9.4 - - + -
197K LEU* 4.0 30.3 - - + -
198K ARG* 5.8 5.2 - - - +
----------------------------------------------------------
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