Contacts of the helix formed by residues 108 - 124 (chain A) in PDB entry 3PEI
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 ASN 108 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASN 3.4 3.5 + - - +
107A ASP* 1.3 73.9 - - - +
109A VAL* 1.3 63.5 + - - +
110A LYS* 3.9 8.0 + - - +
111A GLN* 3.2 36.2 + - - +
112A PHE* 3.2 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE* 3.9 16.6 - - + +
107A ASP 3.4 6.4 + - - +
108A ASN* 1.3 71.1 - - - +
110A LYS* 1.3 57.7 + - - +
112A PHE* 4.3 6.5 - - + -
113A THR* 2.7 41.1 + - - +
146A TYR* 3.4 38.4 - - + +
150A GLN* 3.6 30.5 - - + +
152A ILE* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASN* 3.3 8.5 + - - +
109A VAL* 1.3 77.2 - - - +
111A GLN* 1.3 63.4 + - - +
113A THR* 3.5 1.1 - - - -
114A LEU* 3.0 20.1 + - - +
150A GLN* 4.0 23.6 - - + +
151A ASP* 3.3 34.4 + - - +
152A ILE* 4.5 5.8 - - + -
155A SER* 3.2 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASN* 3.2 27.0 + - - +
110A LYS* 1.3 78.3 - - - +
112A PHE* 1.3 58.8 + - - +
114A LEU* 3.3 16.3 + - - +
115A ASP* 2.9 61.6 + - - +
392A ALA* 3.2 32.3 + - - +
393A SER* 4.1 0.2 - - - +
394A ASN* 5.2 2.0 - - - +
472A HIS* 3.1 34.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
17A ILE* 4.2 9.4 - - + -
66A LEU* 4.3 7.6 - - + -
72A PHE* 5.0 7.0 - + - -
77A TYR* 3.3 38.1 - + - -
100A ILE* 3.8 30.1 - - + -
103A ALA* 3.8 30.1 - - + -
104A PHE* 5.4 2.2 - + - -
107A ASP* 3.7 29.2 - - + +
108A ASN 3.2 18.3 + - - +
109A VAL* 3.8 7.4 - - + +
111A GLN* 1.3 78.6 - - - +
113A THR* 1.3 54.8 + - - +
115A ASP* 3.4 6.4 + - + +
116A THR* 2.8 46.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE* 3.8 12.4 - - - +
109A VAL 2.7 26.3 + - - -
110A LYS 3.5 4.3 - - - -
112A PHE* 1.3 70.7 - - - +
114A LEU* 1.3 66.4 + - - +
116A THR* 3.3 5.2 + - - -
117A VAL* 3.1 24.6 + - - +
144A LEU* 3.9 22.4 - - + -
152A ILE* 3.6 42.6 - - + +
155A SER* 4.2 3.1 - - - -
156A ALA* 4.0 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS 3.0 13.6 + - - +
111A GLN* 3.5 17.7 - - - +
113A THR* 1.3 74.5 - - - +
115A ASP* 1.3 69.0 + - - +
117A VAL* 3.6 0.8 + - - +
118A ARG* 2.9 37.7 + - + +
155A SER* 3.4 28.7 + - - +
158A ILE* 3.8 23.6 - - + -
159A GLY* 3.5 19.5 - - - +
162A ILE* 4.3 7.9 - - + -
472A HIS* 3.7 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 4.1 18.1 - - + -
111A GLN* 2.9 47.4 + - - +
112A PHE* 3.8 6.6 - - + +
114A LEU* 1.3 80.5 - - - +
116A THR* 1.3 55.7 + - - +
118A ARG* 3.8 19.0 + - - +
119A ALA* 2.8 37.2 + - - +
393A SER* 4.0 14.2 - - - +
394A ASN* 4.0 14.0 + - - -
472A HIS* 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.9 17.9 - - + -
77A TYR* 2.8 31.6 + - - +
81A ILE* 4.9 3.2 - - + +
98A VAL* 3.9 17.0 - - + -
100A ILE* 4.5 3.1 - - + -
112A PHE* 2.8 35.5 + - - -
113A THR* 3.3 6.7 + - - -
115A ASP* 1.3 70.4 - - - +
117A VAL* 1.3 67.0 + - - +
119A ALA* 4.0 1.1 - - - +
120A LEU* 3.0 32.4 + - + +
144A LEU* 4.3 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.4 15.0 - - + -
113A THR 3.1 16.7 + - - +
114A LEU 3.9 3.1 - - - +
116A THR* 1.3 77.9 - - - +
118A ARG* 1.3 63.1 + - - +
120A LEU* 3.3 6.0 + - - +
121A ILE* 3.1 42.6 + - + +
142A ILE* 4.6 9.6 - - + -
144A LEU* 3.7 23.8 - - + -
156A ALA* 3.7 38.1 - - + +
160A SER* 3.8 8.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
77A TYR* 5.8 0.8 - - - -
78A ASP* 2.7 42.0 + - - -
114A LEU* 2.9 25.4 + - - +
115A ASP* 3.8 28.6 + - - +
117A VAL* 1.3 77.1 - - - +
119A ALA* 1.3 62.9 + - - +
122A SER* 2.8 32.7 + - - -
159A GLY* 3.4 24.0 + - - +
162A ILE* 3.5 20.9 - - - -
163A ALA* 3.4 11.2 - - + +
166A GLN* 2.8 41.2 + - - +
393A SER 5.4 0.4 + - - -
468A PRO* 4.3 6.6 - - - +
472A HIS* 6.0 0.6 + - - -
501A FMT 3.4 25.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 4.8 2.5 - - + -
78A ASP* 3.7 28.5 - - - +
81A ILE* 3.8 29.6 - - + -
115A ASP 2.8 22.2 + - - +
116A THR 4.2 0.4 - - - +
118A ARG* 1.3 80.8 - - - +
120A LEU* 1.3 54.6 + - - +
122A SER* 4.2 2.2 - - - -
123A GLU* 2.7 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.4 13.9 - - + -
81A ILE* 3.7 21.7 - - + +
84A ALA* 5.2 0.2 - - + -
85A ALA* 5.1 5.4 - - + +
88A LEU* 3.8 28.3 - - + -
96A ILE* 5.0 2.5 - - + -
98A VAL* 3.6 36.8 - - + -
116A THR* 3.0 25.0 + - + +
117A VAL* 3.7 4.5 - - - +
119A ALA* 1.3 78.0 - - - +
121A ILE* 1.3 58.8 + - - +
123A GLU* 4.1 0.4 - - - -
124A THR* 2.8 35.3 + - + +
139A LEU* 4.1 4.6 - - + +
142A ILE* 4.2 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 3.9 17.7 - - + -
3A ILE* 4.1 15.9 - - + -
117A VAL* 3.1 34.1 + - + +
120A LEU* 1.3 74.3 - - - +
122A SER* 1.3 66.5 - - - +
124A THR* 3.4 13.9 + - - -
125A TYR 3.7 1.4 + - - -
139A LEU* 5.0 0.4 - - + -
142A ILE* 3.9 13.2 - - + -
160A SER* 4.0 20.2 - - - +
163A ALA* 3.5 21.3 - - + -
164A CYS* 4.6 1.6 - - + +
167A ASN* 3.2 22.1 + - - +
505A CL 4.2 7.9 - - + -
507A EDO 3.6 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP* 4.5 3.5 + - - -
118A ARG* 2.8 21.8 + - - -
119A ALA* 3.7 5.8 - - - -
121A ILE* 1.3 79.0 - - - +
123A GLU* 1.3 65.2 + - - +
125A TYR* 3.1 15.6 - - - +
163A ALA* 4.0 3.6 - - - +
166A GLN* 3.9 24.8 + - - -
167A ASN* 3.6 11.2 - - - +
170A LYS* 2.9 37.4 + - - -
463A SER 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP* 3.6 46.0 - - + +
81A ILE* 4.6 2.0 - - + -
82A ALA* 3.6 20.8 - - - +
85A ALA* 3.6 23.2 - - + +
119A ALA 2.7 24.7 + - - +
120A LEU 4.6 0.2 - - - +
122A SER* 1.3 78.8 + - - +
124A THR* 1.3 59.6 + - - +
125A TYR* 3.3 4.2 + - - +
170A LYS* 5.6 1.0 + - - -
461A LYS* 3.9 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA* 3.6 27.8 - - + +
88A LEU* 4.5 5.6 - - + -
89A LYS* 6.5 0.2 - - - -
120A LEU 2.8 23.0 + - - +
121A ILE 3.4 0.2 + - - -
123A GLU* 1.3 75.1 - - - +
125A TYR* 1.3 64.1 + - - +
126A VAL* 3.5 12.9 - - - +
137A TYR* 4.2 27.7 - - + +
139A LEU* 3.8 15.3 - - + +
507A EDO 2.7 39.9 + - - -
----------------------------------------------------------
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