Contacts of the strand formed by residues 116 - 124 (chain A) in PDB entry 2HR6
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 ARG 116 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP* 3.0 44.9 + - + -
33A LEU 3.4 7.0 - - - -
34A ARG* 3.7 44.1 - - + +
71A ARG* 3.0 49.0 + - - +
74A LEU* 3.6 6.6 - - - +
114A GLY 3.5 0.4 + - - -
115A GLU* 1.3 76.8 + - - +
117A ILE* 1.3 60.0 + - - +
118A ALA 3.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 3.0 9.6 + - - +
35A ALA* 4.3 14.8 - - + +
51A VAL* 4.9 1.6 - - + -
70A PRO* 5.2 1.4 - - - +
71A ARG* 4.3 5.3 + - - +
74A LEU* 3.8 18.5 - - + +
80A ILE* 4.5 21.5 - - + +
82A LEU* 5.4 2.1 - - - +
99A ILE* 3.7 31.5 - - + +
101A VAL* 4.2 22.9 - - + +
109A PHE* 5.5 3.6 - - + -
111A ILE* 4.5 16.2 - - + -
115A GLU* 3.9 13.7 - - + +
116A ARG* 1.3 72.8 - - - +
118A ALA* 1.3 62.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP* 3.4 6.2 - - - +
33A LEU* 2.8 26.5 + - + +
68A MET* 4.6 6.5 - - + -
69A LEU 3.6 13.5 - - - +
70A PRO* 5.0 0.2 - - + -
71A ARG* 3.8 14.2 - - - +
82A LEU* 4.3 8.7 - - + -
99A ILE* 4.1 30.5 - - + -
116A ARG 3.7 0.8 - - - -
117A ILE* 1.3 80.9 - - - +
119A GLN* 1.3 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY* 4.7 12.1 + - - -
31A LEU 3.2 14.6 - - - +
32A ASP* 3.7 13.3 - - - +
33A LEU* 4.3 3.3 - - - +
68A MET* 3.3 5.9 - - - +
69A LEU* 2.9 53.3 + - + +
70A PRO 3.0 20.5 + - - +
71A ARG* 3.8 13.3 - - + +
72A SER* 4.3 7.1 - - - +
118A ALA* 1.3 76.6 - - - +
120A MET* 1.3 63.0 + - - +
121A ILE* 5.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 6.3 0.2 - - + -
23A TYR* 5.0 0.3 + - - -
30A GLY* 3.2 2.3 - - - -
31A LEU* 2.9 49.0 + - + +
33A LEU* 4.2 16.2 - - + -
57A ILE* 4.3 5.8 - - + -
66A ALA* 3.9 23.3 - - + -
67A MET 3.3 14.6 - - - +
68A MET* 4.0 17.3 - - + -
69A LEU* 5.8 0.2 - - - -
89A ILE* 4.3 5.2 - - - -
97A LEU* 4.0 29.4 - - + -
119A GLN* 1.3 78.5 - - - +
121A ILE* 1.3 66.2 + - - +
122A PHE* 3.7 30.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 5.6 0.2 - - - -
29A ALA* 3.5 31.6 - - + +
30A GLY* 3.8 8.7 - - - -
66A ALA* 3.1 6.4 - - - +
67A MET* 2.8 60.1 + - + +
69A LEU* 4.6 22.7 - - + -
119A GLN* 5.9 2.7 - - + -
120A MET* 1.3 76.3 - - - +
122A PHE* 1.3 64.2 + - - +
123A VAL* 3.5 26.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.4 35.9 - - + -
23A TYR* 3.7 24.4 + - - +
29A ALA 4.9 1.6 + - - -
31A LEU* 4.8 11.9 - - + -
57A ILE* 3.9 18.2 - - + -
59A ILE* 4.0 7.9 - - + -
64A LEU* 4.2 18.5 - - + +
65A ALA 3.3 10.1 - - - +
66A ALA* 3.8 18.8 - - + -
120A MET* 3.7 29.2 - - + -
121A ILE* 1.3 77.8 - - - +
123A VAL* 1.3 65.3 + - - +
124A PRO* 4.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.3 5.9 - - - +
65A ALA* 3.0 34.5 + - + +
66A ALA* 5.3 0.7 - - - -
67A MET* 3.5 29.2 - - + -
88A LEU* 6.4 0.2 - - + -
121A ILE* 3.5 31.4 - - + +
122A PHE* 1.3 76.5 - - - +
124A PRO* 1.3 78.9 - - + +
125A VAL* 4.0 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.8 19.3 - - + -
63A SER 3.3 12.6 - - - +
64A LEU* 3.8 8.0 - - + -
122A PHE 4.6 2.0 - - - +
123A VAL* 1.3 91.7 - - + +
125A VAL* 1.3 64.2 + - - +
126A VAL* 5.8 0.9 - - + -
----------------------------------------------------------
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