Contacts of the helix formed by residues 103 - 113 (chain A) in PDB entry 3Q41
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 THR 103 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 4.7 5.5 - - + -
68A LYS 4.1 13.8 + - - +
69A PRO* 4.6 9.3 + - - +
74A MET* 3.7 28.5 - - + -
92A VAL* 5.1 3.4 - - + -
93A SER 5.1 0.2 - - - +
94A HIS* 4.2 20.9 - - + -
100A ASP* 2.9 28.8 + - - +
102A PHE* 1.3 76.1 - - - +
104A PRO* 1.3 62.2 - - + +
106A PRO* 3.1 24.5 - - - +
107A VAL* 3.7 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 3.6 31.4 - - + +
94A HIS* 3.8 9.4 - - - +
101A HIS 3.8 7.9 - - - +
102A PHE 3.1 6.3 - - - +
103A THR* 1.3 92.5 - - - +
105A THR* 1.3 53.8 + - - +
106A PRO 3.4 0.4 - - - -
107A VAL* 3.0 6.1 + - + +
108A SER* 2.7 34.8 + - - -
123A THR* 3.6 24.2 - - + -
128A TYR* 3.4 11.4 - - + +
137A PHE* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 5.9 0.2 - - - +
102A PHE* 2.7 31.5 + - + +
104A PRO* 1.3 73.0 - - - +
106A PRO* 1.4 65.7 - - - +
108A SER* 3.4 0.9 + - - -
109A TYR* 2.9 46.7 + - + +
127A ILE* 5.3 3.4 - - + -
128A TYR* 3.0 36.1 + - + +
134A HIS* 3.8 18.4 - - + +
72B ILE* 5.8 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 3.7 39.3 - - + +
74A MET* 4.0 13.7 - - + -
75A ALA* 4.2 15.8 - - + +
102A PHE 3.8 0.9 - - - +
103A THR* 3.1 22.0 - - - +
105A THR* 1.4 99.9 - - - +
107A VAL* 1.3 55.4 + - - +
109A TYR* 4.1 6.9 - - + +
110A THR* 3.0 35.2 + - - +
109B TYR* 5.0 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 4.4 9.9 - - + -
74A MET* 4.0 19.1 - - + -
78A VAL* 3.9 27.3 - - + +
90A ILE* 4.0 17.0 - - + -
92A VAL* 3.5 33.7 - - + -
103A THR 3.7 18.2 - - - +
104A PRO* 3.0 6.5 + - + +
106A PRO* 1.3 75.8 - - - +
108A SER* 1.3 57.1 + - - +
110A THR* 3.4 0.6 + - - -
111A ALA* 3.0 35.7 + - - +
118A VAL* 4.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO 2.7 19.7 + - - -
105A THR 3.9 1.1 - - - -
107A VAL* 1.3 74.1 - - - +
109A TYR* 1.3 58.1 + - - +
112A GLY* 2.9 27.2 + - - -
118A VAL* 4.0 11.4 - - - +
128A TYR* 4.8 0.7 - - - -
134A HIS* 2.8 41.9 + - - +
136A SER* 4.7 4.0 + - - -
137A PHE* 3.8 28.0 + - - +
113B PHE* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A THR* 2.9 33.6 + - + +
106A PRO 4.1 1.1 - - - +
108A SER* 1.3 76.3 - - - +
110A THR* 1.3 58.0 + - - +
112A GLY* 3.4 0.9 + - - -
113A PHE* 3.0 27.9 + - - +
133A ILE* 3.7 23.7 - - + +
134A HIS* 3.6 27.2 + + - -
71B ALA 4.9 1.2 + - - -
72B ILE* 5.9 0.2 - - - -
75B ALA* 3.3 27.4 - - + +
106B PRO* 4.9 7.1 - - + +
109B TYR* 3.5 66.4 - + + +
110B THR* 4.3 13.0 - - - -
113B PHE* 5.3 6.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 3.5 25.1 - - - +
78A VAL* 3.8 21.1 - - + -
79A CYS* 3.7 30.5 - - - -
83A ILE* 3.9 2.4 - - + +
106A PRO 3.0 22.7 + - - -
107A VAL 4.0 1.6 - - - -
109A TYR* 1.3 76.0 - - - +
111A ALA* 1.3 57.9 + - - +
113A PHE* 3.3 21.0 - - - +
114A TYR* 3.8 11.7 - - + -
109B TYR* 4.0 9.7 - - - -
133B ILE* 3.8 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 4.7 0.9 - - + -
83A ILE* 4.2 11.4 - - + -
90A ILE* 4.3 17.0 - - + -
107A VAL 3.0 16.0 + - - +
110A THR* 1.3 73.1 - - - +
112A GLY* 1.3 63.8 + - - +
113A PHE 3.1 2.0 - - - -
114A TYR* 3.2 4.5 + - - +
115A ARG 3.2 2.8 + - - -
116A ILE* 3.0 45.4 + - + +
118A VAL* 3.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A SER 2.9 22.2 + - - -
109A TYR 3.8 0.7 - - - -
111A ALA* 1.3 75.7 - - - +
113A PHE* 1.3 59.4 + - - +
114A TYR 3.1 0.7 - - - -
115A ARG* 2.9 30.8 + - - -
116A ILE 4.2 0.6 + - - -
136A SER* 3.7 22.0 - - - -
113B PHE* 3.1 18.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR 3.0 12.4 + - - +
110A THR* 3.3 17.5 - - - +
111A ALA 3.1 0.2 - - - -
112A GLY* 1.3 77.3 - - - +
114A TYR* 1.3 82.5 + + - +
115A ARG* 3.7 3.3 + - - +
311A ASN 4.1 3.8 - - - -
312A THR* 4.4 2.5 - - + -
314A ILE* 3.7 2.8 - - - +
109B TYR* 5.4 5.8 - + + -
112B GLY* 2.9 40.8 - - - -
113B PHE* 4.3 4.3 - - - +
115B ARG* 2.7 67.4 + - - +
133B ILE 4.9 7.9 - - - +
135B LEU* 3.7 38.4 - - + -
136B SER* 4.4 6.5 - - - -
----------------------------------------------------------
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