Contacts of the helix formed by residues 106 - 119 (chain A) in PDB entry 1H9T
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 106 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 2.8 22.4 + - - +
103A SER* 4.2 6.2 - - - +
104A VAL 2.7 2.8 - - - -
105A ARG* 1.3 93.9 + - - +
107A ASN* 1.3 81.1 - - - +
108A ILE 2.9 0.2 - - - -
109A SER* 2.0 31.6 + - - -
110A THR 3.3 0.7 + - - -
212A VAL* 3.6 31.2 - - + +
213A ARG* 4.8 7.0 - - - -
216A GLY* 4.4 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A SER* 3.0 33.2 + - - -
104A VAL 3.5 1.1 + - - +
106A THR* 1.3 88.1 - - - +
108A ILE* 1.3 57.7 + - + +
110A THR* 2.3 36.2 + - - -
209A TYR* 5.4 2.4 - - - -
213A ARG* 3.0 37.1 + - - +
111B ILE* 3.4 38.4 - - + +
115B THR* 5.6 2.8 + - - -
161B TYR* 3.0 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 2.8 44.6 + - + +
105A ARG* 4.5 3.4 - - - -
106A THR 2.6 3.6 + - - -
107A ASN* 1.3 72.4 - - - +
109A SER* 1.3 69.0 + - - +
111A ILE* 2.7 25.0 + - + +
112A PHE* 3.5 8.0 + - + -
161A TYR* 4.1 27.8 - - + -
164A ILE* 5.1 4.9 - - + -
165A LEU* 5.6 6.7 - - + -
168A MET* 4.6 5.6 - - + -
108B ILE* 4.9 15.9 - - + -
111B ILE* 4.2 9.4 - - + -
161B TYR* 4.2 18.4 - - + -
164B ILE* 4.1 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG 2.6 19.9 + - - -
106A THR* 2.0 35.7 + - - -
108A ILE* 1.3 72.6 - - - +
110A THR* 1.3 55.6 + - - -
112A PHE* 2.8 25.0 + - - -
113A ILE* 2.7 53.9 + - - +
149A PHE* 4.0 11.6 - - - -
212A VAL* 3.3 11.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
106A THR 3.7 1.3 - - - +
107A ASN* 2.3 31.2 + - - +
108A ILE 2.9 1.6 + - - -
109A SER* 1.3 71.7 + - - +
111A ILE* 1.3 73.0 + - - +
113A ILE* 4.3 4.7 - - - -
114A ARG* 3.3 23.6 + - - +
208A VAL* 3.5 21.7 - - - +
209A TYR* 4.2 29.8 - - + -
212A VAL* 3.3 33.9 - - + -
213A ARG* 4.9 3.8 - - + +
111B ILE* 4.6 1.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
108A ILE* 2.7 20.1 + - - +
110A THR* 1.3 86.5 + - - +
112A PHE* 1.3 61.6 + - - +
114A ARG* 3.4 6.1 - - - +
115A THR* 3.3 24.2 + - - +
161A TYR* 3.2 28.7 - - + +
107B ASN* 3.1 53.8 - - + +
108B ILE* 3.7 7.6 - - + +
111B ILE* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG 5.1 0.9 - - - -
108A ILE* 3.5 8.5 + - + -
109A SER* 2.8 41.2 + - - -
111A ILE* 1.3 75.0 - - - +
113A ILE* 1.3 70.9 + - + +
115A THR* 4.2 2.9 - - - -
116A ALA* 2.9 25.9 + - - +
149A PHE* 3.6 29.2 - + + -
152A LEU* 3.4 15.0 - - + -
153A ALA* 2.9 44.2 - - + -
156A SER* 3.1 18.8 - - - -
161A TYR* 3.7 37.9 - + + -
165A LEU* 4.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A SER* 2.7 56.3 + - - +
110A THR* 3.8 5.6 - - - +
112A PHE* 1.3 84.6 - - + +
114A ARG* 1.3 59.2 + - - +
116A ALA* 3.4 9.9 - - + +
117A PHE* 2.7 47.6 - - + -
149A PHE* 4.5 11.9 - - + -
152A LEU* 4.0 21.3 - - + -
192A PHE* 5.2 4.7 - - + -
196A LEU* 4.8 14.1 - - + -
208A VAL* 4.8 9.0 - - + -
212A VAL* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A THR 3.3 15.9 + - - +
111A ILE* 3.4 6.3 - - - +
113A ILE* 1.3 78.5 - - - +
115A THR* 1.3 72.0 + - - +
117A PHE* 2.9 23.0 + - - +
118A ARG* 3.4 11.0 + - - +
205A HIS* 4.0 44.9 + - + +
206A ASP* 4.9 4.2 - - - +
208A VAL* 4.3 21.4 - - + +
209B TYR* 5.4 10.6 + - - -
213B ARG* 5.9 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 3.3 17.6 + - - +
112A PHE* 4.2 1.5 - - - -
113A ILE 3.4 0.2 - - - -
114A ARG* 1.3 84.6 + - - +
116A ALA* 1.3 63.6 + - - +
117A PHE 2.8 1.6 + - - -
118A ARG* 3.1 26.2 + - - +
119A GLN* 3.1 23.2 + - + +
156A SER* 2.8 41.7 - - - +
158A ASN* 5.6 2.5 - - + +
161A TYR* 6.4 2.0 - - + -
107B ASN* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE 2.9 21.2 + - - +
113A ILE* 3.4 11.7 - - - +
115A THR* 1.3 75.0 - - - +
117A PHE* 1.3 58.5 + - + +
119A GLN 2.5 19.1 - - - +
120A HIS 3.6 9.5 - - - +
124A ALA* 3.7 12.4 - - + +
152A LEU* 4.4 13.7 - - + +
155A ALA* 4.1 10.8 - - + +
156A SER* 3.1 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 2.7 42.6 - - + -
114A ARG* 2.9 10.6 + - - +
115A THR 2.8 1.4 + - - -
116A ALA* 1.3 76.7 - - + +
118A ARG* 1.3 68.7 + - - +
119A GLN 2.7 3.6 + - - -
121A PRO* 2.8 33.0 - - + +
124A ALA* 4.9 7.4 - - + -
125A GLN* 5.7 0.7 - - - -
128A LEU* 6.6 0.2 - - + -
152A LEU* 6.0 3.6 - - + -
196A LEU* 3.6 25.8 - - + -
197A SER* 5.6 0.2 - - - -
199A LEU* 3.2 20.6 - - + -
200A CYS* 2.9 49.1 - - + -
203A GLY* 5.2 0.7 - - - -
204A ALA 5.7 0.4 - - - -
205A HIS* 3.7 20.9 - + + +
208A VAL* 5.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 3.4 7.5 + - - +
115A THR* 3.1 31.3 + - - +
117A PHE* 1.3 79.0 - - - +
119A GLN* 1.3 105.1 + - - +
121A PRO* 3.9 6.6 - - - +
205A HIS* 3.1 28.6 + - + +
213B ARG* 5.4 7.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
115A THR* 3.1 9.6 + - + +
116A ALA 2.5 27.4 - - - +
117A PHE 2.7 1.6 + - - -
118A ARG* 1.3 118.4 + - - +
120A HIS* 1.3 84.1 + - + +
121A PRO* 3.3 1.6 - - - -
155A ALA 3.5 1.6 - - - +
156A SER 4.6 7.0 - - - +
157A GLY* 5.7 0.2 - - - -
----------------------------------------------------------
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