Contacts of the helix formed by residues 103 - 119 (chain A) in PDB entry 3QOW
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 103 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 4.1 7.4 - - - -
101A ARG 3.7 1.6 + - - -
102A PRO* 1.3 76.0 - - - +
104A THR* 1.3 53.9 + - - +
105A GLY* 3.5 3.5 + - - -
106A LEU* 2.9 28.2 + - - +
107A LEU* 2.8 33.7 + - - +
211A LYS* 5.4 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO 3.8 0.2 + - - -
103A SER* 1.3 72.1 - - - +
105A GLY* 1.3 59.8 + - - +
107A LEU* 3.3 7.7 + - - +
108A ARG* 3.0 30.5 + - - +
141A PHE* 3.5 30.8 - - + -
145A ALA* 5.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 3.4 34.3 - - - -
103A SER* 3.3 3.6 + - - -
104A THR* 1.3 77.5 - - - +
106A LEU* 1.3 62.6 + - - +
108A ARG* 3.5 10.1 + - - +
109A HIS* 3.4 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 3.6 42.6 - - + +
47A GLU* 4.0 13.0 - - + +
102A PRO* 3.7 20.4 - - + -
103A SER* 2.9 22.3 + - - +
105A GLY* 1.3 72.5 - - - +
107A LEU* 1.3 67.0 + - - +
109A HIS* 3.1 4.7 + - + +
110A ILE* 2.9 35.1 + - + +
209A TYR* 4.0 21.1 - - + -
211A LYS* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 4.1 17.4 - - + +
103A SER 2.8 20.3 + - - +
104A THR* 3.6 7.9 - - - +
106A LEU* 1.3 73.1 - - - +
108A ARG* 1.3 62.2 + - - +
110A ILE* 3.2 8.0 + - + -
111A LEU* 2.9 55.4 + - + +
141A PHE* 4.1 7.0 - - + -
172A GLN* 3.7 34.1 - - + +
175A ALA* 3.6 27.4 - - + +
176A ALA* 4.4 12.1 - - + -
202A PHE* 4.5 6.7 - - + -
206A MET* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR* 3.0 20.3 + - - +
105A GLY* 3.8 9.9 - - - +
106A LEU 3.3 0.2 - - - -
107A LEU* 1.3 75.3 - - - +
109A HIS* 1.3 62.7 + - - +
111A LEU* 3.5 2.3 + - - +
112A GLN* 3.1 24.8 + - + +
141A PHE* 3.6 49.9 - - + +
142A ASP* 2.9 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 3.8 11.0 - - + -
39A GLU* 3.6 29.2 - - + +
40A THR* 2.9 32.3 + - - -
43A TRP* 3.6 34.2 + + + +
105A GLY 3.4 4.1 + - - +
106A LEU* 3.1 10.1 + - + +
108A ARG* 1.3 77.7 - - - +
110A ILE* 1.3 66.7 + - - +
112A GLN* 3.3 7.7 + - - +
113A GLN* 2.9 31.7 + - + +
209A TYR* 3.0 22.0 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 4.4 5.4 - - + -
106A LEU* 2.9 44.1 + - + +
107A LEU* 3.2 9.2 + - + +
109A HIS* 1.3 76.9 - - - +
111A LEU* 1.3 58.0 + - + +
113A GLN* 3.1 9.2 + - - +
114A VAL* 2.8 46.6 + - + +
202A PHE* 4.3 10.8 - - + -
205A TRP* 4.4 11.7 - - + -
206A MET* 3.8 32.5 - - + -
209A TYR* 3.6 35.2 - - + -
211A LYS* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 2.9 33.3 + - + +
108A ARG* 4.0 3.6 - - - +
110A ILE* 1.3 73.5 - - - +
112A GLN* 1.3 61.0 + - - +
114A VAL* 3.9 4.5 - - + +
115A TYR* 2.9 29.5 + - - +
141A PHE* 3.9 16.2 - - + -
168A GLN* 4.4 14.2 - - + +
171A LEU* 3.8 34.1 - - + -
172A GLN* 3.6 30.3 - - + +
198A MET* 5.1 2.8 - - + +
202A PHE* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASP* 5.3 0.2 - - - +
31A HIS* 3.1 38.6 + - + +
108A ARG* 3.1 19.1 + - + +
109A HIS* 3.3 8.5 + - - +
111A LEU* 1.3 75.9 - - - +
113A GLN* 1.3 57.2 + - - +
115A TYR* 3.3 11.6 + - - +
116A ASN* 2.8 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.5 2.2 + - - -
36A GLU* 3.0 40.2 + - + +
40A THR* 3.0 23.1 + - - -
109A HIS* 2.9 18.0 + - + +
110A ILE* 3.3 9.6 - - - +
112A GLN* 1.3 77.5 - - - +
114A VAL* 1.3 62.0 + - - +
116A ASN* 3.5 1.2 + - - -
117A HIS* 3.0 30.7 + - + -
205A TRP* 3.3 42.2 - - + +
209A TYR* 2.8 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 2.8 33.0 + - + +
111A LEU* 3.9 6.5 - - - +
113A GLN* 1.3 70.3 - - - +
115A TYR* 1.3 63.8 + - - +
117A HIS* 3.4 1.9 + - - +
118A SER* 2.6 31.0 + - - -
171A LEU* 4.3 3.1 - - + -
198A MET* 3.6 42.6 - - + +
201A GLU* 3.8 15.0 - - + +
202A PHE* 3.6 33.2 - - + +
205A TRP* 3.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU 2.9 18.9 + - - +
112A GLN* 3.3 11.6 + - - +
114A VAL* 1.3 77.5 - - - +
116A ASN* 1.3 69.5 + - - +
118A SER 3.0 0.5 + - - -
119A VAL* 2.8 66.6 + - + +
122A PRO* 4.9 12.5 - - + +
125A LEU* 3.7 13.9 - - + +
138A GLU* 2.7 39.9 + - - -
166A VAL* 3.9 15.0 - - + -
168A GLN* 5.1 8.3 - - + -
198A MET* 3.7 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.4 66.7 - - + +
28A ASP* 3.9 11.1 + - - -
31A HIS* 3.8 7.0 + - - -
36A GLU* 4.4 2.4 - - - +
112A GLN* 2.8 50.5 + - - +
113A GLN* 3.9 3.3 - - - +
115A TYR* 1.3 82.2 - - - +
117A HIS* 1.3 60.6 + - - +
118A SER 3.6 0.3 + - - -
119A VAL 4.4 10.0 - - - +
120A THR* 5.2 3.1 + - - +
122A PRO* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL 5.7 3.1 - - - -
20A TYR* 4.2 14.4 - + - -
27A TYR* 3.6 12.0 + + - -
36A GLU* 2.7 36.3 + - - -
113A GLN* 3.0 34.5 + - + +
114A VAL 3.9 2.5 - - - +
116A ASN* 1.3 75.3 - - - +
118A SER* 1.3 59.8 + - - +
120A THR* 4.4 11.7 - - - +
197A THR* 4.5 2.9 - - - +
201A GLU* 3.5 34.5 + - - +
204A LYS* 5.0 2.1 + - - -
205A TRP* 3.8 16.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL 2.6 20.6 + - - -
115A TYR 3.0 2.2 + - - -
117A HIS* 1.3 78.5 - - - +
119A VAL* 1.3 63.3 + - - +
120A THR* 3.1 11.8 + - - +
194A TYR* 3.4 16.8 - - - -
197A THR* 3.7 17.4 + - - +
198A MET* 3.4 41.2 - - - -
201A GLU* 3.3 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TYR* 2.8 60.7 + - + +
116A ASN* 4.4 7.6 - - - +
118A SER* 1.3 71.6 - - - +
120A THR* 1.3 63.0 + - - +
122A PRO* 3.5 34.8 - - + +
125A LEU* 3.9 17.9 - - + -
166A VAL* 4.5 14.1 - - + -
194A TYR* 4.1 17.0 - - + -
198A MET* 4.1 11.7 - - - -
----------------------------------------------------------
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