Contacts of the helix formed by residues 119 - 138 (chain A) in PDB entry 2PEG
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 119 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PRO 5.2 1.6 - - - +
116A LYS* 3.5 20.2 - - - +
117A GLU* 2.9 10.5 + - - +
118A PHE* 1.3 75.7 - - - +
120A PRO* 1.4 70.8 - - + +
121A GLU* 3.3 14.8 + - - +
122A ALA* 3.0 20.3 + - - +
123A HIS* 2.9 27.2 + - - +
30B ARG* 3.6 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A THR* 1.4 88.5 - - + +
121A GLU* 1.3 65.1 + - - +
123A HIS* 3.3 3.6 + - + +
124A VAL* 2.9 25.6 + - - +
26B LYS 5.6 0.7 - - - +
29B SER* 5.9 0.4 - - - -
30B ARG* 3.5 47.1 - - + +
33B ILE* 3.7 42.9 - - + +
34B VAL* 3.9 1.8 - - + +
55B ILE* 4.5 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 6.4 1.3 - - - -
9A ALA* 4.9 3.4 - - - +
119A THR* 3.3 22.1 + - - +
120A PRO* 1.3 81.0 - - - +
122A ALA* 1.3 60.9 + - - +
124A VAL* 3.3 24.0 - - + +
125A SER* 3.6 9.4 + - - -
33B ILE* 3.7 16.4 - - + +
51B ALA* 2.9 36.6 - - + +
55B ILE* 3.7 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 5.2 11.0 - - - +
13A LEU* 4.3 17.8 - - + +
117A GLU 3.5 19.1 - - - +
118A PHE* 4.2 10.8 - - + -
119A THR* 3.0 21.5 + - - +
121A GLU* 1.3 76.2 - - - +
123A HIS* 1.3 57.8 + - - +
125A SER* 3.9 1.4 - - - -
126A LEU* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 4.0 10.3 - - + +
118A PHE* 3.6 24.7 - + + -
119A THR 2.9 16.6 + - - +
120A PRO 3.4 6.1 - - - +
122A ALA* 1.3 75.3 - - - +
124A VAL* 1.4 60.0 + - - +
127A ASP* 2.8 35.3 + - + +
30B ARG* 2.9 40.3 + - + +
34B VAL* 3.5 27.7 - - + +
35B TYR* 5.2 3.0 + - - -
109B CYS* 4.7 7.2 - - - -
112B ILE* 3.5 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASP* 5.4 0.7 - - - +
120A PRO 2.9 19.0 + - - +
121A GLU* 3.3 19.1 - - - +
123A HIS* 1.4 71.9 - - - +
125A SER* 1.3 71.5 + - - +
127A ASP* 3.3 2.3 + - - +
128A LYS* 2.9 46.3 + - + +
33B ILE* 3.5 27.8 - - + +
34B VAL* 3.6 28.2 - - + +
36B PRO* 5.0 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.4 2.3 - - - +
5A LYS* 4.5 4.7 + - - +
6A ASP* 2.7 43.6 + - - -
9A ALA* 3.7 29.3 - - - +
10A VAL* 3.7 5.5 - - - +
121A GLU 3.6 8.4 + - - -
122A ALA 3.6 2.7 + - - -
123A HIS 3.3 0.2 - - - -
124A VAL* 1.3 82.6 - - - +
126A LEU* 1.3 57.5 + - - +
128A LYS* 3.4 3.3 + - - +
129A PHE* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.1 19.0 - - + +
13A LEU* 3.8 24.0 - - + -
14A TRP* 6.2 3.6 - - + -
67A ILE* 6.2 1.6 - - + -
71A VAL* 6.2 0.2 - - + -
106A ILE* 5.5 0.2 - - + -
107A LEU* 3.7 24.2 - - + -
110A ILE* 3.7 26.0 - - + -
118A PHE* 3.8 8.5 - - + -
122A ALA 2.9 19.3 + - - +
123A HIS 4.0 2.2 - - - +
125A SER* 1.3 77.3 - - - +
127A ASP* 1.3 57.1 + - - +
129A PHE* 3.3 27.4 + - + +
130A LEU* 2.8 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASN* 6.1 0.9 - - - +
107A LEU* 3.9 20.7 - - + +
123A HIS* 2.8 30.9 + - + +
124A VAL 3.6 4.0 - - - +
126A LEU* 1.3 71.5 - - - +
128A LYS* 1.3 61.6 + - - +
130A LEU* 3.8 6.8 - - - +
131A SER* 2.9 38.9 + - - -
34B VAL* 4.2 7.9 - - + +
35B TYR* 3.9 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A ACE 3.9 23.8 - - + +
1A SER 3.1 21.5 + - - -
2A LEU* 3.7 14.7 - - + +
3A SER* 4.7 2.6 + - - +
6A ASP* 2.8 34.2 + - - +
124A VAL* 2.9 32.3 + - + +
125A SER 3.8 2.2 - - - +
127A ASP* 1.3 77.0 - - + +
129A PHE* 1.3 58.3 + - - +
131A SER* 3.3 8.3 + - - -
132A GLY* 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 3.6 16.3 - - + +
10A VAL* 3.7 14.8 - - + -
67A ILE* 4.2 11.0 - - + -
70A ALA* 3.5 42.6 - - + -
71A VAL* 3.7 23.1 - - + -
74A ILE* 3.6 32.5 - - + -
77A LEU* 4.2 5.0 - - + +
125A SER 3.0 14.6 + - - +
126A LEU* 3.4 26.7 - - + +
128A LYS* 1.3 76.2 - - - +
130A LEU* 1.3 70.2 + - + +
132A GLY* 3.0 3.8 + - - -
133A VAL* 2.8 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 3.9 28.3 - - + -
103A ASN* 3.0 55.0 + - + +
106A ILE* 4.5 13.9 - - + -
107A LEU* 3.5 33.7 - - + -
126A LEU* 2.8 25.5 + - + +
127A ASP* 3.4 6.7 + - - +
129A PHE* 1.3 83.5 - - + +
131A SER* 1.3 60.2 + - - +
133A VAL* 3.5 4.6 - - + +
134A ALA 2.8 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASN* 4.7 1.3 - - - +
127A ASP* 2.9 24.2 + - - -
128A LYS* 3.5 11.3 - - - -
130A LEU* 1.3 75.5 - - - +
132A GLY* 1.3 58.6 + - - +
134A ALA* 3.3 7.2 + - - +
135A LEU* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 5.9 2.0 - - - -
77A LEU* 3.7 16.6 - - - +
128A LYS 2.9 14.0 + - - -
129A PHE* 3.0 5.3 + - - -
131A SER* 1.3 73.1 - - - +
133A VAL* 1.3 59.9 + - - +
135A LEU* 3.3 8.8 + - - +
136A ALA* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 4.4 17.5 - - + -
70A ALA* 3.8 13.0 - - + -
77A LEU* 4.3 6.3 - - + -
81A LEU* 3.8 18.6 - - + -
103A ASN* 5.1 1.3 - - - +
129A PHE* 2.8 50.6 + - + +
130A LEU* 3.2 13.0 + - + +
132A GLY* 1.3 75.2 - - - +
134A ALA* 1.3 58.7 + - - +
136A ALA* 3.2 3.1 + - - +
137A LEU* 2.8 44.0 + - + +
200A HEM 4.7 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 3.8 27.3 - - + -
100A LYS* 4.7 6.5 - - + +
103A ASN* 3.7 14.3 - - - +
130A LEU 2.8 16.9 + - - +
131A SER* 3.3 7.6 + - - +
133A VAL* 1.3 79.1 - - - +
135A LEU* 1.3 55.6 + - - +
137A LEU* 3.3 5.6 + - - +
138A ALA* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER 2.9 17.0 + - - +
132A GLY* 3.7 8.1 - - - +
133A VAL 3.3 0.2 - - - -
134A ALA* 1.3 76.7 - - - +
136A ALA* 1.3 62.4 + - - +
138A ALA* 3.2 19.8 + - + +
139A GLU* 3.3 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 3.6 35.2 - - + +
78A LYS* 4.1 8.8 - - + +
81A LEU* 3.9 15.7 - - + +
85A SER* 3.6 6.6 - - - -
132A GLY 2.9 18.1 + - - +
133A VAL 3.5 4.7 - - - +
135A LEU* 1.3 73.7 - - - +
137A LEU* 1.3 65.5 + - - +
138A ALA 3.1 0.4 - - - -
139A GLU* 3.0 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.4 13.9 - - + -
84A LEU* 3.8 34.1 - - + +
85A SER* 2.6 30.5 + - - +
88A HIS* 4.7 6.1 - - + +
99A PHE* 3.8 29.9 - - + -
133A VAL* 2.8 32.5 + - + +
134A ALA* 3.8 4.9 - - - +
136A ALA* 1.3 75.9 - - - +
138A ALA* 1.3 57.7 + - - +
141A TYR* 3.2 15.2 - - - -
200A HEM 3.5 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PRO* 4.8 11.4 - - + -
99A PHE* 4.3 2.7 - - + -
134A ALA 3.0 16.9 + - - +
135A LEU* 3.5 16.8 - - + +
136A ALA 3.1 0.4 - - - -
137A LEU* 1.3 78.6 - - - +
139A GLU* 1.3 63.6 + - - +
140A ARG 3.4 1.1 - - - -
141A TYR* 3.0 31.1 + - + +
142A ARG* 4.5 2.4 + - - +
----------------------------------------------------------
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