Contacts of the strand formed by residues 114 - 125 (chain Q) in PDB entry 5HJD
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 VAL 114 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115N ASN* 5.1 1.6 + - - -
15Q HIS* 3.5 38.6 - - + +
16Q ARG* 3.1 24.4 - - - +
17Q ALA* 3.1 28.1 + - + +
105Q PHE* 4.0 19.5 - - + +
106Q LEU 4.3 0.2 - - - -
107Q HIS* 3.5 49.4 - - + +
113Q PRO* 1.3 74.7 - - - +
115Q ASN* 1.3 64.2 + - - +
116Q HIS 4.2 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N ARG* 6.2 2.2 - - - +
37N ARG* 4.6 8.8 + - - -
115N ASN* 3.2 55.5 + - - +
116N HIS 4.6 1.0 + - - -
117N LEU* 3.2 35.8 - - + +
15Q HIS 3.7 5.9 - - - +
16Q ARG* 3.8 18.4 + - - +
35Q PHE* 5.5 4.3 - - - -
113Q PRO 3.8 3.0 + - - +
114Q VAL* 1.3 75.5 - - - +
116Q HIS* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 116 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N GLU* 6.2 3.8 - - - -
117N LEU* 4.3 1.5 - - - +
14Q GLY* 3.2 20.6 - - - -
15Q HIS* 3.0 32.0 + - + +
35Q PHE* 4.7 2.1 - - - -
102Q TYR* 3.4 27.9 - + - +
103Q ASP 5.4 0.2 - - - -
105Q PHE* 4.0 27.0 - + + -
114Q VAL* 4.4 0.9 - - + -
115Q ASN* 1.3 76.6 + - - +
117Q LEU* 1.3 79.0 + - - +
118Q ARG* 4.3 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N GLU* 5.2 8.3 + - + +
39N PRO* 6.2 0.2 - - - +
117N LEU* 3.4 50.2 - - + +
118N ARG 4.3 0.4 - - - -
119N CYS* 4.0 22.7 - - + +
12Q GLU* 4.0 24.2 - - + +
13Q LEU 3.7 14.8 - - - +
35Q PHE* 4.0 13.9 - - + -
37Q ARG* 3.6 19.3 - - - +
116Q HIS* 1.3 87.2 + - - +
118Q ARG* 1.3 62.3 + - - +
119Q CYS* 4.2 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q GLU* 3.6 1.4 - - - -
13Q LEU* 2.6 65.4 + - + +
100Q PHE* 3.6 23.3 - - - +
101Q ASP 3.4 21.2 + - - -
102Q TYR* 4.0 23.0 - - + +
103Q ASP* 4.7 2.0 - - - +
116Q HIS* 4.3 15.3 - - + +
117Q LEU* 1.3 75.1 - - - +
119Q CYS* 1.3 63.3 + - - +
120Q GLU* 3.1 22.9 + - - +
201Q SO4 2.2 36.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 119 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119N CYS* 2.0 54.1 - - + -
10Q LYS* 6.4 1.1 - - + -
11Q LEU 3.6 6.1 - - - +
12Q GLU* 3.8 15.0 - - - -
117Q LEU* 4.2 6.3 - - - -
118Q ARG* 1.3 74.6 - - - +
120Q GLU* 1.3 73.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q VAL 4.0 0.2 - - - +
10Q LYS* 3.5 3.1 - - - -
11Q LEU* 2.7 46.5 + - + +
13Q LEU* 3.8 20.0 - - + -
100Q PHE* 3.6 37.9 - - + -
118Q ARG* 3.1 26.9 + - - +
119Q CYS* 1.3 84.0 - - - +
121Q LYS* 1.3 64.2 + - - +
122Q LEU* 4.1 1.6 + - + +
201Q SO4 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121N LYS* 5.0 4.5 - - - +
202N SO4 2.6 40.7 + - - +
8Q GLN* 2.8 44.9 + - - +
9Q VAL 3.4 7.6 - - - +
10Q LYS* 4.3 15.3 - - + +
120Q GLU* 1.3 76.6 + - - +
122Q LEU* 1.3 67.6 + - - +
123Q THR* 4.2 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Q VAL 3.4 1.9 - - - +
8Q GLN* 3.2 6.2 - - - -
9Q VAL* 2.8 54.5 + - + +
11Q LEU* 3.6 30.5 - - + -
47Q PHE* 5.2 0.4 - - + -
89Q PHE* 4.0 28.0 - - + -
98Q VAL* 4.1 16.2 - - + -
100Q PHE* 3.8 26.2 - - + -
120Q GLU* 4.8 2.5 - - + +
121Q LYS* 1.3 80.6 - - - +
123Q THR* 1.3 61.7 + - - +
124Q PHE* 3.9 9.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Q ALA* 4.1 17.5 - - + -
7Q VAL 3.4 4.0 - - - +
8Q GLN* 3.8 32.1 + - + +
121Q LYS* 4.2 8.0 + - - +
122Q LEU* 1.3 74.2 - - - +
124Q PHE* 1.3 63.7 + - - +
125Q ASN* 3.8 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Q ALA* 3.6 1.6 - - - -
7Q VAL* 2.7 42.1 + - + +
9Q VAL* 3.9 18.2 - - + -
89Q PHE* 3.5 48.9 - + - -
95Q PRO* 4.3 26.0 - - + -
122Q LEU* 4.0 13.2 - - + -
123Q THR* 1.3 75.9 - - - +
125Q ASN* 1.3 62.6 + - - +
127Q PRO* 3.6 14.8 - - + +
131Q PHE* 3.6 23.6 - + - -
135Q LEU* 3.8 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 125 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q CYS 3.6 3.1 - - - +
6Q ALA* 4.2 9.0 - - - +
93Q GLU* 4.9 4.5 - - - +
123Q THR* 4.0 26.7 + - - +
124Q PHE* 1.3 70.7 - - - +
126Q ASN* 1.3 80.5 + - - +
127Q PRO* 3.4 1.2 - - - +
----------------------------------------------------------
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