Contacts of the strand formed by residues 136 - 143 (chain B) in PDB entry 3HKS
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 ILE 136 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLN* 3.5 6.6 - - - +
92B LEU* 2.9 54.5 + - + -
125B GLN 4.5 6.1 - - - +
126B MET* 4.8 3.1 - - - +
129B GLY* 3.8 31.9 - - - -
130B PHE 4.2 2.2 - - - +
134B LYS* 3.7 22.7 - - + +
135B ASP* 1.3 73.3 - - - +
137B VAL* 1.3 63.7 + - - +
138B VAL* 4.1 6.7 - - + -
152B VAL* 3.8 22.9 - - + -
153B LYS 3.4 13.0 - - - +
154B GLU* 4.2 12.8 - - + +
155B VAL* 5.2 0.2 - - - +
161B EDO 3.3 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASP* 3.7 37.5 - - + +
90B TYR 3.4 8.5 - - - +
91B GLN* 4.4 15.7 - - + -
136B ILE* 1.3 77.5 - - - +
138B VAL* 1.3 64.3 + - - +
139B SER* 5.3 1.4 + - - +
151B ALA 4.7 0.2 - - - -
152B VAL* 3.5 2.1 - - - -
153B LYS* 2.8 69.3 + - + +
155B VAL* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL 3.6 0.9 - - - +
89B ASP* 3.3 3.5 - - - -
90B TYR* 2.9 34.7 + - + +
92B LEU* 4.6 7.4 - - + -
103B LEU* 3.5 36.3 - - + -
126B MET* 3.8 32.8 - - + -
136B ILE* 4.1 15.0 - - + -
137B VAL* 1.3 78.4 - - - +
139B SER* 1.3 60.3 + - - +
140B VAL* 3.9 8.9 + - + -
149B ILE* 4.2 15.0 - - + -
151B ALA 3.4 8.1 - - - +
152B VAL* 4.5 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 3.4 37.3 + - - -
88B VAL 3.5 5.2 - - - -
89B ASP* 2.7 22.2 + - - -
137B VAL* 5.3 1.4 + - - +
138B VAL* 1.3 71.1 - - - +
140B VAL* 1.3 61.3 + - - +
141B MET 4.1 0.2 - - - -
149B ILE* 3.4 5.5 - - - +
150B CYS* 2.9 30.4 + - - -
151B ALA* 2.9 20.7 + - - +
153B LYS* 6.0 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASN 3.5 1.7 - - - +
87B ARG* 3.3 4.4 - - - -
88B VAL* 2.7 42.7 + - + +
90B TYR* 3.6 30.5 - - + +
103B LEU* 4.1 8.5 - - + -
111B LYS* 4.8 0.7 - - - -
114B LEU* 3.9 32.8 - - + -
138B VAL* 4.3 3.4 - - + -
139B SER* 1.3 75.3 - - - +
141B MET* 1.3 69.6 + - - +
142B SER* 4.1 2.1 + - - -
147B GLU* 4.0 21.5 - - + +
148B GLN 3.5 7.9 - - - +
149B ILE* 4.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B HIS* 6.0 1.6 - - + -
64B ILE* 3.9 39.7 - - + +
65B PHE* 3.7 17.4 - - + -
85B VAL* 3.8 19.5 - - + -
86B ASN 3.2 7.4 - - - +
87B ARG* 4.3 26.5 - - + +
139B SER 4.1 1.0 - - - -
140B VAL* 1.3 71.8 - - - +
142B SER* 1.3 64.1 + - - +
147B GLU* 3.2 4.2 - - - -
148B GLN* 2.8 43.5 + - + +
150B CYS* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 4.2 1.3 - - - -
84B HIS 3.9 0.9 - - - +
85B VAL* 3.5 1.9 - - - +
86B ASN* 2.9 53.2 + - - +
88B VAL* 5.9 0.7 - - - +
140B VAL* 5.0 2.9 + - - -
141B MET* 1.3 77.3 - - - +
143B SER* 1.3 63.3 + - - +
146B GLU 3.0 11.2 - - - -
147B GLU* 3.6 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PRO* 3.4 10.4 - - - +
64B ILE* 3.8 25.4 - - - -
65B PHE* 3.7 5.4 - - - -
83B PRO* 3.4 20.8 - - - +
84B HIS 3.0 20.5 + - - -
85B VAL* 3.7 3.3 - - - +
142B SER* 1.3 76.3 - - - +
144B MET* 1.3 71.1 + - - +
145B GLY 3.2 2.9 - - - +
146B GLU* 2.9 23.1 + - - +
----------------------------------------------------------
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