Contacts of the helix formed by residues 100 - 111 (chain A) in PDB entry 3R9X
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 100 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 4.1 6.7 - - - +
97A GLU* 3.5 38.1 - - + +
98A GLY 3.2 0.4 + - - -
99A TRP* 1.3 87.1 + - - +
101A PRO* 1.3 93.7 - - + +
102A ARG* 3.3 3.6 - - + +
103A ASP* 3.0 27.0 + - - +
104A GLU 3.1 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TRP 4.7 0.4 - - - +
100A ARG* 1.3 116.6 - - + +
102A ARG* 1.3 57.4 + - - +
104A GLU* 3.0 9.9 + - + +
105A GLU* 2.9 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 3.8 22.6 - - + +
12A PRO* 3.0 24.4 - - - +
62A ILE 2.8 29.7 + - - -
63A TYR* 3.1 26.4 - - - +
64A GLU* 3.8 7.5 - - - +
100A ARG* 3.3 3.2 - - + +
101A PRO* 1.3 77.0 - - - +
103A ASP* 1.3 66.4 + - - +
105A GLU* 3.7 24.0 - - - +
106A ILE* 3.1 37.0 + - - +
504A MRD 4.4 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 2.7 49.3 + - - +
91A PHE* 3.5 24.2 - - + -
92A MET 4.8 0.9 - - - +
93A ILE* 3.9 20.8 - - + +
98A GLY 3.5 8.5 - - - +
99A TRP* 4.2 14.8 - - + +
100A ARG* 3.0 28.5 + - - +
102A ARG* 1.3 77.1 - - - +
104A GLU* 1.3 58.8 + - - +
106A ILE* 3.4 3.3 + - - -
107A TYR* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TRP* 2.9 22.6 + - + +
100A ARG 3.1 7.8 + - - +
101A PRO* 3.0 13.9 + - + +
103A ASP* 1.3 76.4 - - - +
105A GLU* 1.3 60.8 + - + +
107A TYR* 4.4 1.6 - - - -
108A GLN* 2.7 64.9 + - + +
144A LYS* 3.9 6.4 - - - +
145A HIS* 2.7 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 4.1 4.0 - - - +
101A PRO* 2.9 26.2 + - - +
102A ARG* 3.7 20.7 + - - +
104A GLU* 1.3 77.9 - - + +
106A ILE* 1.3 58.9 + - - +
108A GLN* 4.7 3.1 - - - -
109A ASN* 2.8 40.2 + - - +
504A MRD 2.8 46.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY* 4.0 2.7 - - - +
11A LYS* 3.7 26.2 - - + +
62A ILE* 3.5 63.7 - - + +
91A PHE* 3.7 21.1 - - + -
102A ARG* 3.1 25.1 + - - +
103A ASP* 3.7 4.7 - - - +
104A GLU 3.2 0.2 - - - -
105A GLU* 1.3 77.2 - - - +
107A TYR* 1.3 61.9 + - - +
110A PHE* 3.0 30.4 + - + +
111A ILE* 3.5 10.8 + - + +
504A MRD 4.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 4.1 10.7 - + + -
99A TRP* 3.8 19.3 - + + -
103A ASP 2.9 17.6 + - - +
104A GLU 3.8 2.7 - - - +
106A ILE* 1.3 78.6 - - - +
108A GLN* 1.3 78.6 + - - +
111A ILE* 3.3 26.4 + - + -
112A LYS* 2.8 70.1 + - + +
118A VAL* 5.0 4.2 - - + +
145A HIS* 3.8 32.1 - + - -
147A GLU* 2.6 23.1 + - - +
148A LEU* 3.7 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 2.7 51.2 + - + +
105A GLU* 4.0 2.7 - - - +
107A TYR* 1.3 91.0 - - - +
109A ASN* 1.3 70.5 + - - +
112A LYS* 4.2 17.6 + - - +
113A PRO* 3.3 22.0 - - - +
145A HIS* 3.4 19.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU* 2.8 23.8 + - - +
108A GLN* 1.3 86.5 + - - +
110A PHE* 1.3 79.0 + - + +
113A PRO* 4.2 9.7 - - - +
504A MRD 3.0 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 3.9 28.0 - - + -
76A VAL* 3.9 11.7 - - + -
80A LYS* 3.7 39.7 - - + -
83A LEU* 3.8 16.6 - - + +
106A ILE* 3.0 21.4 + - - +
109A ASN* 1.3 91.9 - - + +
111A ILE* 1.3 67.3 + - + +
113A PRO* 4.1 3.6 - - - -
114A LEU* 3.4 22.2 - - - +
504A MRD 3.2 55.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.5 32.3 - - + -
83A LEU* 4.7 4.5 - - + -
89A ILE* 4.1 14.0 - - + +
91A PHE* 3.6 32.8 - - + -
106A ILE* 3.7 13.9 - - + +
107A TYR* 3.3 19.1 + - + +
110A PHE* 1.3 86.6 - - + +
112A LYS* 1.3 69.6 + - - +
113A PRO* 3.0 4.4 - - - +
114A LEU* 3.1 20.7 + - - +
115A ASN 4.2 1.7 + - - -
116A LYS 5.4 0.9 + - - -
118A VAL* 3.6 32.5 - - + +
----------------------------------------------------------
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