Contacts of the strand formed by residues 213 - 219 (chain B) in PDB entry 1KWV
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 HIS 213 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 3.2 20.4 + - - -
119B MET* 2.8 28.0 + - - +
124B VAL* 4.5 0.2 - - - +
154B SER* 2.7 36.9 + - - +
156B PHE* 3.5 38.2 - + + +
197B THR* 3.6 22.4 - - + +
207B ILE* 4.0 15.0 - - + +
211B ALA* 3.8 18.7 - - + +
212B SER* 1.3 88.7 + - - +
214B THR* 1.3 67.1 + - - +
215B ALA 3.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 3.3 23.1 - - + +
116B HIS* 4.2 12.5 - - - -
117B GLU 3.4 10.1 - - - +
118B ARG* 3.5 14.6 + - - +
151B ALA 4.6 8.5 - - - +
153B THR* 2.9 26.5 + - - +
154B SER 2.9 16.9 + - - -
155B ALA* 3.2 25.0 - - + +
156B PHE* 3.4 10.7 + - - +
213B HIS* 1.3 71.1 - - - +
215B ALA* 1.3 63.3 + - - +
216B VAL* 3.6 10.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 3.9 6.6 - - + -
114B THR* 2.4 32.4 + - - -
115B ASN* 4.1 6.6 + - - +
117B GLU 2.9 17.0 + - - +
119B MET* 4.0 16.4 - - + -
124B VAL* 3.9 31.2 - - + -
127B LEU* 4.5 9.9 - - + -
213B HIS 3.5 0.4 + - - -
214B THR* 1.3 71.7 - - - +
216B VAL* 1.3 56.4 + - - +
217B CYS* 4.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 4.5 6.1 - - + -
113B VAL 3.5 17.3 - - - +
114B THR* 3.9 11.9 - - - +
124B VAL* 4.4 3.0 - - - +
128B CYS* 3.9 0.9 - - - -
135B VAL* 3.7 9.2 - - - +
136B ALA* 2.9 40.4 + - + +
147B ILE* 4.6 10.1 - - + -
150B VAL* 4.4 9.4 - - + -
151B ALA* 4.0 16.8 - - + +
155B ALA* 3.9 25.4 - - + -
156B PHE 5.1 4.0 + - - +
214B THR* 3.6 4.0 + - + -
215B ALA* 1.3 79.7 - - - +
217B CYS* 1.3 68.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 4.0 24.5 - - + -
111B PHE 3.7 0.4 - - - +
112B PHE* 3.4 4.2 - - - -
113B VAL* 3.0 32.4 + - - +
127B LEU* 4.7 1.6 - - - -
128B CYS* 2.0 54.3 - - + -
131B LEU* 4.4 5.8 - - - -
134B THR 3.3 6.5 - - - +
136B ALA* 4.3 1.3 - - - -
215B ALA* 5.3 0.9 - - - -
216B VAL* 1.3 79.9 - - - +
218B GLU* 1.3 61.7 - - - +
219B PHE* 4.1 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LYS* 2.9 38.1 + - + +
111B PHE 3.2 4.9 - - - +
112B PHE* 3.4 21.4 - - + -
133B GLY* 3.6 4.3 - - - -
134B THR* 2.9 47.1 + - - +
135B VAL 4.3 1.3 - - - -
136B ALA* 4.0 3.4 - - - -
137B ILE* 2.9 34.0 + - - +
139B ARG* 5.4 3.6 + - - -
217B CYS* 1.3 73.9 - - - +
219B PHE* 1.3 72.8 + - - +
220B PRO* 4.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.7 29.4 - - + -
110B LYS* 3.4 9.1 - - - +
111B PHE* 2.8 62.3 + + + +
113B VAL* 3.6 25.1 - - + -
131B LEU* 3.2 36.8 - - + -
132B ARG 4.1 4.9 - - - -
133B GLY* 3.5 18.6 - - - -
217B CYS* 4.1 15.5 - - + -
218B GLU* 1.3 79.4 - - - +
220B PRO* 1.3 74.1 - - + +
----------------------------------------------------------
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