Contacts of the helix formed by residues 122 - 142 (chain A) in PDB entry 4WMJ
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 VAL 122 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 5.2 0.7 - - + -
106A ALA* 3.9 27.4 - - + -
115A ILE* 2.9 28.0 + - + +
117A VAL* 3.5 37.7 - - + -
120A LYS* 3.7 11.4 - - - +
121A ASP* 1.3 73.9 - - - +
123A THR* 1.3 69.7 + - + +
124A PRO* 3.3 0.9 - - - -
125A ASP* 3.0 10.1 + - + +
126A VAL* 3.0 22.6 + - + +
272A TRP* 3.7 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA 5.9 0.9 - - - +
109A ASN* 3.1 32.3 - - - +
112A ASN* 4.3 12.3 + - - +
113A ARG 3.1 13.9 - - - +
115A ILE 4.3 1.8 - - - +
121A ASP* 2.9 24.3 + - - +
122A VAL* 1.3 80.2 - - + +
124A PRO* 1.4 74.1 - - - +
126A VAL* 3.2 6.9 + - - +
127A ASN* 2.8 43.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASP* 3.3 26.0 - - + +
122A VAL 3.5 0.9 - - - -
123A THR* 1.4 99.0 - - - +
125A ASP* 1.3 59.6 + - - +
127A ASN* 3.5 6.8 + - + +
128A ALA* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS* 2.6 41.3 + - - +
121A ASP 4.7 0.6 - - - +
122A VAL* 3.0 11.1 + - + +
124A PRO* 1.3 78.2 - - - +
126A VAL* 1.4 65.6 + - + +
128A ALA* 3.4 6.4 + - - +
129A VAL* 3.1 28.2 + - - +
270A TRP* 3.7 27.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA 3.6 26.7 - - - +
107A LEU* 3.8 22.9 - - + +
109A ASN* 5.7 0.4 - - + +
122A VAL* 3.0 22.6 + - + +
123A THR* 3.6 9.2 - - - +
125A ASP* 1.4 74.4 - - - +
127A ASN* 1.3 68.9 + - - +
129A VAL* 3.3 4.3 + - - +
130A LEU* 3.0 33.1 + - + +
270A TRP* 3.7 13.9 - - + -
272A TRP* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASN 5.3 0.7 - - - +
110A ARG* 5.3 2.9 + - - -
112A ASN* 3.0 37.4 + - - +
123A THR* 2.8 23.3 + - - +
124A PRO* 4.0 6.1 - - + +
126A VAL* 1.3 83.2 - - - +
128A ALA* 1.3 56.6 + - - +
130A LEU* 3.4 18.8 + - - +
131A ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO 2.9 18.6 + - - +
125A ASP* 3.7 7.6 - - - +
126A VAL 3.2 0.4 - - - -
127A ASN* 1.3 75.1 - - - +
129A VAL* 1.3 64.9 + - + +
131A ALA* 3.3 7.4 + - - +
132A HIS* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASP 3.1 15.0 + - - +
126A VAL 3.8 6.3 - - - +
128A ALA* 1.3 75.9 - - + +
130A LEU* 1.3 59.5 + - + +
132A HIS* 3.1 9.5 + - + +
133A MET* 2.9 37.6 + - + +
267A PHE* 4.7 5.4 - - + -
268A GLY* 3.6 38.8 - - - +
270A TRP* 3.7 16.8 - - + -
282A ALA* 4.0 20.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
107A LEU 4.3 3.8 - - - +
110A ARG* 4.0 23.1 - - - +
126A VAL* 3.0 30.2 + - + +
127A ASN* 3.6 21.5 - - - +
128A ALA 3.3 0.2 - - - -
129A VAL* 1.3 78.1 - - + +
131A ALA* 1.3 57.5 + - - +
133A MET* 3.4 12.1 + - - -
134A LYS* 2.9 25.3 + - - +
280A TRP 4.8 6.5 - - - +
281A SER* 5.8 1.1 - - - -
293A PHE* 3.4 25.8 - - + -
296A PHE* 4.0 16.6 - - + -
300A LEU* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN 2.9 16.9 + - - +
128A ALA* 3.3 8.7 + - - +
130A LEU* 1.3 75.0 - - - +
132A HIS* 1.3 56.8 + - - +
134A LYS* 3.4 11.6 + - + +
135A GLU* 3.0 28.8 + - - +
293A PHE* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA 3.1 11.6 + - - +
129A VAL* 3.1 12.9 + - - +
131A ALA* 1.3 74.3 - - - +
133A MET* 1.3 64.3 + - - +
135A GLU* 3.3 19.7 + - - +
136A PHE* 2.9 25.2 + - + +
264A LYS* 3.2 29.0 + - - +
265A ASN* 4.6 2.6 + - - -
266A MET 3.7 19.3 + - - -
267A PHE* 3.3 35.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 2.9 22.5 + - + +
130A LEU* 3.4 26.0 - - - +
132A HIS* 1.3 77.7 - - - +
134A LYS* 1.3 53.3 + - - +
136A PHE* 4.0 0.7 - - - +
137A SER* 2.7 39.4 + - - -
267A PHE* 3.9 22.0 - - + -
281A SER 3.6 14.4 - - - +
282A ALA* 3.8 21.5 - - - -
284A GLY 3.8 4.7 - - - +
285A LEU* 3.6 42.1 - - + +
288A SER* 4.7 3.1 - - - +
293A PHE* 4.2 7.9 - - + -
296A PHE* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU 2.9 17.5 + - - +
131A ALA* 3.5 10.1 - - + +
132A HIS 3.3 0.2 - - - -
133A MET* 1.3 73.8 - - - +
135A GLU* 1.3 59.7 + - - +
137A SER* 3.4 2.3 + - - -
138A THR* 3.0 43.8 + - + +
293A PHE* 3.5 45.5 - - + +
297A GLU* 4.9 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ALA 3.0 16.0 + - - +
132A HIS* 3.3 21.2 + - - +
134A LYS* 1.3 75.1 - - - +
136A PHE* 1.3 65.2 + - - +
138A THR* 2.4 24.8 + - - +
139A GLN* 3.0 37.9 + - + +
264A LYS* 6.0 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A HIS* 2.9 20.9 + - + +
133A MET 4.0 1.6 - - - +
135A GLU* 1.3 78.6 + - - +
137A SER* 1.3 64.3 + - - +
139A GLN* 3.1 10.1 + - - +
140A VAL* 2.9 44.0 + - + +
145A TRP* 3.5 44.4 - + - -
208A LEU* 3.8 23.1 - - + -
247A VAL* 3.9 22.0 - - + -
265A ASN* 5.0 3.6 - - - -
267A PHE* 3.6 24.0 - + + -
285A LEU* 4.1 26.5 - - + -
289A LEU* 4.2 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A MET 2.7 22.0 + - - -
134A LYS* 3.6 6.1 - - - -
136A PHE* 1.3 77.6 - - - +
138A THR* 1.3 58.3 + - - +
140A VAL* 3.2 0.7 + - - +
141A ILE* 2.8 42.0 + - - +
285A LEU* 4.1 5.9 - - - +
288A SER* 2.7 43.0 + - - -
289A LEU* 3.8 14.0 + - - +
293A PHE* 4.6 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 3.0 25.4 + - + +
135A GLU* 2.4 28.1 + - - +
137A SER* 1.3 75.5 - - - +
139A GLN* 1.3 56.7 + - - +
141A ILE* 4.1 5.1 - - - +
142A SER* 2.8 40.3 + - - -
293A PHE* 6.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLU* 3.0 41.9 + - + +
136A PHE* 3.1 12.6 + - - +
138A THR* 1.3 83.3 + - - +
140A VAL* 1.3 61.6 + - - +
142A SER* 3.9 3.8 - - - -
143A GLY 3.3 1.4 + - - -
144A ALA* 3.0 24.2 + - + -
145A TRP* 3.0 54.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 2.9 49.2 + - + +
139A GLN* 1.3 77.8 - - - +
141A ILE* 1.3 64.3 + - - +
143A GLY* 3.2 11.6 + - - -
145A TRP* 4.0 20.8 - - + +
152A PRO* 5.6 0.3 - - - +
153A ILE* 3.9 40.8 + - + +
156A VAL* 5.0 0.7 - - + -
181A HIS* 5.0 0.5 + - - -
182A LEU* 4.1 11.9 - - + +
208A LEU* 4.1 8.5 - - + -
289A LEU* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER* 2.8 32.1 + - - +
138A THR* 4.1 4.3 - - - +
140A VAL* 1.3 74.7 - - - +
142A SER* 1.3 60.4 + - - +
143A GLY* 3.5 0.9 + - - -
180A ASN* 3.5 24.2 - - + +
181A HIS* 3.2 34.8 + - + -
182A LEU* 3.9 10.8 - - + -
288A SER 4.1 12.6 - - - +
289A LEU* 3.5 24.2 - - + +
292A GLY* 4.2 10.3 - - - -
293A PHE 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A THR* 2.8 24.5 + - - -
139A GLN* 3.4 1.0 + - - -
141A ILE* 1.3 77.2 - - - +
143A GLY* 1.3 59.6 + - - +
144A ALA* 3.4 19.4 + - - +
----------------------------------------------------------
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