Contacts of the helix formed by residues 103 - 120 (chain A) in PDB entry 1IW1
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
----------------------------------------------------------
48A GLN* 3.0 17.8 + - - +
101A THR 3.5 2.0 + - - -
102A ALA* 1.3 76.2 - - - +
104A PRO* 1.3 76.6 - - - +
105A ALA* 3.4 8.7 + - - +
106A VAL* 3.0 25.7 + - - +
107A ILE* 2.9 20.8 + - - +
207A VAL* 5.1 1.9 + - - +
210A ASP* 4.1 15.9 - - - +
211A LEU* 5.8 2.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
102A ALA 4.5 0.9 - - - +
103A SER* 1.3 88.8 - - - +
105A ALA* 1.3 62.1 + - - +
107A ILE* 3.3 13.2 + - + +
108A ASP* 3.2 18.0 + - - +
210A ASP* 3.7 15.9 - - + +
470B LYS* 3.5 35.6 - - + +
474B ASP* 5.5 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A SER* 3.1 4.0 - - - +
104A PRO* 1.3 77.0 - - - +
106A VAL* 1.3 60.3 + - - +
108A ASP* 3.3 8.6 + - - +
109A TYR* 3.0 26.4 + - - +
203A PHE* 4.7 3.9 - - - +
206A GLN* 3.5 41.5 - - + +
207A VAL* 3.5 14.6 - - + +
210A ASP* 3.0 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 3.1 41.7 - - + +
51A LEU* 3.9 17.3 - - + -
52A PHE* 4.3 9.4 - - + +
102A ALA* 3.8 15.0 - - + -
103A SER* 3.0 13.7 + - - +
105A ALA* 1.3 75.6 - - - +
107A ILE* 1.3 58.0 + - - +
109A TYR* 4.1 4.3 - - - -
110A VAL* 2.8 46.9 + - + +
207A VAL* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA* 3.8 24.5 - - + +
103A SER 2.9 18.7 + - - +
104A PRO* 3.3 12.3 + - + +
106A VAL* 1.3 76.6 - - - +
108A ASP* 1.3 57.6 + - - +
110A VAL* 3.9 3.4 - - - +
111A ASN* 2.9 51.6 + - - +
914A SO4 3.6 23.8 - - - +
470B LYS* 3.7 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO 3.2 5.9 + - - +
105A ALA* 3.6 9.5 - - - +
107A ILE* 1.3 80.2 - - - +
109A TYR* 1.3 61.9 + - - +
111A ASN* 3.4 10.5 + - - +
112A ARG* 3.0 23.6 + - - +
203A PHE* 4.0 18.9 - - + -
467B ALA 4.7 1.1 - - - +
468B LYS* 3.4 9.0 - - + +
469B LEU* 3.2 24.9 + - - +
470B LYS* 2.8 52.5 + - - +
471B VAL* 5.3 0.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
52A PHE* 3.5 41.1 - + + -
56A LEU* 5.7 0.3 - - - +
105A ALA 3.0 16.5 + - - +
106A VAL* 3.7 5.4 - - - +
108A ASP* 1.3 73.6 - - - +
110A VAL* 1.3 63.4 + - - +
112A ARG* 3.2 4.0 + - - +
113A LEU* 3.0 40.9 + - + +
128A HIS* 3.8 26.3 + + - +
132A ARG* 3.3 23.9 - - - +
200A ALA* 4.9 1.7 - - - +
203A PHE* 3.7 37.0 - + + -
204A ASN* 2.9 38.2 + - - -
207A VAL* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.8 23.3 - - + +
52A PHE* 4.0 8.1 - - + -
55A ALA* 4.0 13.7 - - + -
102A ALA* 5.8 1.3 - - + -
106A VAL* 2.8 40.6 + - + +
107A ILE* 3.9 4.0 - - - +
109A TYR* 1.3 72.0 - - - +
111A ASN* 1.3 58.0 + - - +
113A LEU* 3.2 3.0 + - - +
114A GLU* 2.9 55.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 2.9 30.1 + - - +
108A ASP* 3.7 10.4 + - - +
109A TYR 3.3 0.2 - - - -
110A VAL* 1.3 78.4 - - - +
112A ARG* 1.3 62.8 + - - +
114A GLU* 3.3 17.0 + - - +
115A GLU* 3.0 23.8 + - - +
914A SO4 2.8 38.3 + - - -
445B ARG* 4.7 16.2 + - - +
469B LEU* 6.3 3.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASP 3.0 14.4 + - - +
109A TYR 3.2 7.4 + - - +
111A ASN* 1.3 76.5 - - - +
113A LEU* 1.3 59.3 + - - +
115A GLU* 2.8 44.1 + - - +
116A ILE* 2.9 37.3 + - + +
119A ASN* 5.5 1.8 - - - +
121A ASP* 4.7 5.0 + - - -
124A ALA* 4.7 1.0 - - - +
128A HIS* 4.3 6.3 - - + +
192A HIS* 4.0 19.0 + - - -
196A GLU* 2.8 43.6 + - - +
199A ASP* 5.8 0.8 + - - -
203A PHE* 3.9 26.5 - - + -
462B HIS* 4.0 25.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.5 30.3 - - + +
55A ALA* 3.9 19.3 - - + +
56A LEU* 3.7 21.8 - - + +
59A ALA* 3.7 8.7 - - + +
109A TYR* 3.0 40.3 + - + +
110A VAL 3.7 5.4 - - - +
112A ARG* 1.3 75.0 - - - +
114A GLU* 1.3 57.4 + - - +
116A ILE* 3.3 9.1 + - + +
117A ARG* 2.9 27.0 + - - +
125A LEU* 5.6 0.9 - - + -
128A HIS* 3.6 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 4.5 10.1 - - + +
58A GLN* 4.7 4.7 - - - +
110A VAL* 2.9 38.8 + - + +
111A ASN* 3.7 17.5 - - - +
113A LEU* 1.3 73.4 - - - +
115A GLU* 1.3 60.0 + - - +
117A ARG* 3.3 35.3 + - - +
118A ASP* 2.8 37.5 + - - +
907A SO4 5.0 7.7 + - - -
445B ARG* 6.3 3.1 - - - -
449B ARG* 5.7 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASN 3.0 13.5 + - - +
112A ARG* 2.8 44.6 + - - +
114A GLU* 1.3 74.1 - - - +
116A ILE* 1.3 59.1 + - + +
118A ASP* 3.8 6.9 - - - +
119A ASN* 2.9 54.7 + - - +
441B GLN* 5.2 5.8 - - - +
444B ALA* 6.1 1.0 - - - +
445B ARG* 6.4 3.6 - - + +
461B TYR 5.8 0.3 - - - +
462B HIS* 4.8 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA* 4.4 8.3 - - + -
63A VAL* 4.9 1.8 - - + +
112A ARG* 2.9 31.3 + - + +
113A LEU* 3.3 11.6 + - + +
115A GLU* 1.3 75.2 - - - +
117A ARG* 1.3 58.7 + - - +
119A ASN* 4.7 0.2 - - - -
120A VAL* 2.8 24.1 + - - -
121A ASP* 3.0 39.5 + - + +
124A ALA* 3.7 20.6 - - + +
125A LEU* 3.8 20.0 - - + +
128A HIS* 3.4 38.6 - - + +
196A GLU* 3.9 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA 5.4 0.7 - - - +
58A GLN* 3.1 55.0 + - + +
59A ALA* 3.7 16.2 - - - +
62A ALA* 3.9 12.4 - - + +
63A VAL* 5.8 0.2 - - - -
113A LEU 2.9 14.7 + - - +
114A GLU* 3.5 32.5 + - - +
115A GLU 3.2 0.2 - - - -
116A ILE* 1.3 76.9 - - - +
118A ASP* 1.3 86.6 + - - +
120A VAL* 3.0 26.7 + - - +
907A SO4 4.5 12.9 + - - -
449B ARG* 4.0 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 2.8 25.6 + - - +
115A GLU* 3.3 6.6 + - - +
117A ARG* 1.3 99.6 + - - +
119A ASN* 1.3 62.3 + - - +
120A VAL* 3.2 6.1 + - - +
445B ARG* 4.7 7.6 - - - +
448B GLN* 3.0 23.4 + - + +
449B ARG* 3.0 35.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 5.5 1.6 - - - +
115A GLU* 2.9 41.8 + - - +
116A ILE* 4.2 2.4 - - - +
118A ASP* 1.3 76.9 - - - +
120A VAL* 1.3 70.4 + - - +
121A ASP* 3.2 15.9 + - + +
448B GLN* 3.0 27.8 + - - +
455B PRO* 3.5 30.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 3.8 20.9 - - + +
63A VAL* 4.0 13.2 - - + -
66A SER* 3.7 30.9 + - - +
116A ILE 2.8 11.3 + - - -
117A ARG 3.0 15.2 + - - +
118A ASP 4.0 6.1 - - - +
119A ASN* 1.3 81.5 - - - +
121A ASP* 1.3 56.8 + - - +
122A GLY 3.2 7.2 + - - -
----------------------------------------------------------
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