Contacts of the strand formed by residues 115 - 123 (chain B) in PDB entry 4HJU
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 115 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 4.5 5.7 + - - -
118A THR 2.7 24.5 + - - -
119A THR* 3.5 14.8 - - - -
201A 16L 5.3 0.2 - - - +
88B HIS* 3.8 4.9 - - - -
112B SER* 2.8 44.1 + - - +
114B TYR* 1.3 79.3 - - - +
116B TYR* 1.3 69.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU 3.0 25.8 + - - -
93A VAL* 4.5 2.8 - - - -
116A TYR* 4.2 20.0 - + - +
117A SER* 3.5 1.3 - - - -
118A THR* 2.9 45.8 + - + +
75B THR* 5.7 2.2 - - + -
88B HIS* 3.8 39.3 - + + -
90B HIS 4.4 2.1 + - - -
91B ALA* 3.7 38.8 - - + -
92B GLU 3.9 5.5 + - - -
93B VAL* 5.8 0.9 - - + -
109B ALA* 5.7 1.6 - - + -
110B LEU 3.2 13.0 - - - +
111B LEU* 4.0 16.2 - - + -
115B SER* 1.3 79.9 + - - +
117B SER* 1.3 71.4 + - - +
118B THR* 4.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 5.5 2.0 - - - -
116A TYR 3.4 11.0 - - - -
117A SER* 4.1 14.8 - - - -
109B ALA* 3.2 5.0 - - - +
110B LEU* 2.8 46.7 + - - +
116B TYR* 1.3 78.1 - - - +
118B THR* 1.3 63.4 + - - +
201B 16L 2.8 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A HIS* 4.2 7.9 - - - +
115A SER* 2.7 25.0 + - - -
116A TYR* 2.9 62.0 + - + +
93B VAL* 3.6 24.9 - - + +
107B ILE* 4.2 4.5 - - - +
108B ALA 2.8 19.0 + - - -
109B ALA* 4.4 5.6 - - - +
116B TYR* 4.9 6.5 - - + -
117B SER* 1.3 75.4 - - - +
119B THR* 1.3 59.8 + - - +
201B 16L 3.8 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A HIS* 5.0 3.1 - - - -
114A TYR* 3.3 15.9 + - - +
115A SER* 3.4 14.5 - - - -
93B VAL* 6.6 0.2 - - - -
106B THR 3.8 0.2 - - - +
107B ILE* 3.7 5.1 - - - +
108B ALA* 3.0 41.8 + - + +
118B THR* 1.3 77.8 + - - +
120B ALA* 1.3 70.4 + - - +
121B VAL* 4.5 14.8 - - + -
201B 16L 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 3.4 51.8 - - + -
114A TYR* 3.1 21.2 + - + +
106B THR 3.3 7.2 - - - +
107B ILE* 4.4 2.2 - - + -
119B THR* 1.3 84.6 + - - +
121B VAL* 1.3 64.5 + - - +
122B VAL* 4.0 7.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ARG 3.5 3.1 - - - +
105B TYR* 3.7 0.2 - - - -
106B THR* 2.9 49.0 + - + +
108B ALA* 5.5 2.5 - - + -
119B THR* 4.5 15.0 - - + +
120B ALA* 1.3 76.0 - - - +
122B VAL* 1.3 61.4 + - - +
123B THR* 4.0 19.9 + - + +
201B 16L 4.2 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 3.9 19.5 - - + -
114A TYR* 4.4 13.9 - - + -
101B GLY* 5.5 0.2 - - - -
102B PRO* 3.4 49.4 - - + +
104B ARG 3.2 7.4 - - - +
105B TYR* 3.9 31.4 - - + +
120B ALA* 4.0 10.9 + - + -
121B VAL* 1.3 77.3 - - - +
123B THR* 1.3 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PRO* 3.2 8.7 - - - +
103B ARG 2.9 4.9 + - - -
104B ARG* 2.8 52.1 + - - +
121B VAL* 4.0 22.7 + - + -
122B VAL* 1.3 78.7 - - - +
124B ASN* 1.3 61.9 + - - +
----------------------------------------------------------
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