Contacts of the helix formed by residues 114 - 129 (chain A) in PDB entry 2WJP
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 GLY 114 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 1.3 75.9 - - - +
115A LYS* 1.3 57.4 + - - +
117A THR* 3.8 0.5 - - - -
118A VAL* 2.9 34.0 + - - +
177A LEU* 3.4 7.4 - - - -
271A ASN* 4.0 20.2 - - - -
1448A SO4 2.8 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 3.8 16.7 - - + +
110A THR* 4.0 9.2 - - - -
111A GLY 3.3 25.8 + - - +
112A SER 4.9 5.2 + - - -
113A ASN 3.3 3.2 + - - -
114A GLY* 1.3 77.9 - - - +
116A SER* 1.3 59.1 + - - +
119A THR* 2.7 34.4 + - - -
138A ASN* 4.0 11.1 - - - +
157A GLU* 3.2 37.7 - - + +
158A LEU 3.8 15.7 - - - +
159A SER* 4.5 1.7 - - - +
177A LEU* 3.7 7.6 - - + -
183A HIS* 5.7 2.8 + - - -
198A KCX 3.2 25.2 + - - -
319A LYS* 6.0 2.2 - - - +
1448A SO4 3.5 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LYS* 1.3 75.6 - - - +
117A THR* 1.3 61.5 + - - +
119A THR* 3.8 0.7 - - - -
120A THR* 2.8 35.7 + - - -
139A ILE* 3.4 18.2 - - - +
157A GLU* 2.6 27.2 + - - -
299A LEU* 3.6 11.4 - - - -
302A ARG* 3.3 24.9 + - - -
319A LYS* 4.1 3.5 - - - -
1448A SO4 3.1 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLY 3.8 2.2 - - - -
116A SER* 1.3 73.0 - - - +
118A VAL* 1.3 56.6 + - - +
120A THR* 3.4 2.9 + - - -
121A LEU* 2.9 32.6 + - + +
263A LEU* 4.3 7.9 - - + -
268A ASN* 4.3 10.7 + - - +
271A ASN* 4.0 25.6 + - + +
296A PHE* 4.1 21.6 - - + -
299A LEU* 3.7 14.8 + - - +
302A ARG* 4.4 6.9 - - - +
1448A SO4 2.8 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 4.2 9.2 - - + -
114A GLY 2.9 21.6 + - - +
115A LYS 4.2 1.3 - - - +
117A THR* 1.3 76.0 - - - +
119A THR* 1.3 63.4 + - - +
121A LEU* 3.3 5.8 + - - +
122A VAL* 3.0 24.3 + - - +
177A LEU* 3.6 24.7 - - + -
271A ASN* 3.6 36.3 - - + +
274A ALA 4.5 0.7 - - - -
275A ALA* 4.0 16.2 - - - +
278A LEU* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 3.4 21.8 - - - +
115A LYS 2.7 23.1 + - - -
116A SER 3.8 3.6 - - - -
118A VAL* 1.3 76.7 - - - +
120A THR* 1.3 64.0 + - - +
122A VAL 3.4 0.5 + - - -
123A GLY* 3.1 18.5 + - - -
135A VAL* 3.7 22.5 - - + +
136A GLY 4.5 1.8 - - - +
139A ILE* 4.2 9.2 - - + -
155A VAL* 3.6 18.0 - - + +
157A GLU* 3.4 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER 2.8 19.7 + - - -
117A THR 3.8 2.7 - - - -
119A THR* 1.3 75.9 - - - +
121A LEU* 1.3 57.6 + - - +
123A GLY* 3.2 3.5 + - - +
124A GLU* 2.9 36.1 + - + +
135A VAL* 4.7 7.6 - - - +
139A ILE* 3.9 13.3 - - - +
296A PHE* 3.5 27.4 - - + -
299A LEU* 3.8 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 2.9 31.7 + - + +
118A VAL 3.6 4.3 - - - +
120A THR* 1.3 77.2 - - - +
122A VAL* 1.3 58.3 + - - +
124A GLU* 3.0 7.0 + - + +
125A MET* 2.9 33.7 + - + +
261A MET* 5.8 1.1 - - + -
263A LEU* 4.9 7.0 - - + -
271A ASN* 4.2 4.9 - - + +
272A ALA* 4.1 13.0 - - + +
275A ALA* 3.8 21.5 - - + -
292A ALA 4.5 6.7 - - - +
293A LEU* 4.0 27.8 - - + -
296A PHE* 3.4 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 4.4 15.0 - - + -
109A ILE* 4.5 1.8 - - + -
118A VAL* 3.0 23.2 + - + +
121A LEU* 1.3 72.9 - - - +
123A GLY* 1.3 62.9 + - - +
125A MET* 3.2 9.0 + - - +
126A ALA* 3.0 22.0 + - - +
153A LEU* 5.1 0.9 - - + -
155A VAL* 3.9 28.9 - - + -
275A ALA* 3.7 33.2 - - - +
278A LEU* 4.2 15.9 - - + -
279A ALA* 4.8 15.0 - - - +
284A LEU* 4.4 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A THR 3.1 12.0 + - - -
120A THR 3.2 5.1 + - - -
122A VAL* 1.3 76.7 - - - +
124A GLU* 1.3 60.4 + - - +
126A ALA* 3.3 4.5 + - - +
127A LYS* 3.0 33.6 + - - +
133A VAL* 3.8 4.1 - - - +
135A VAL* 3.9 26.5 - - - -
155A VAL* 4.3 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A THR* 2.9 25.0 + - + +
121A LEU* 3.0 9.1 + - + +
123A GLY* 1.3 74.2 - - - +
125A MET* 1.3 64.8 + - - +
127A LYS* 2.9 40.2 + - - +
128A ALA* 3.0 24.8 + - - +
292A ALA* 3.7 18.6 - - + +
295A THR* 5.4 4.6 + - - +
296A PHE* 4.3 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 2.9 18.4 + - + +
122A VAL* 3.4 11.9 - - - +
124A GLU* 1.3 74.0 - - - +
126A ALA* 1.3 62.4 + - - +
128A ALA* 3.3 4.7 + - - +
129A ALA* 3.2 21.0 + - - +
275A ALA* 3.7 25.6 - - + +
276A LEU* 3.8 13.5 - - + +
279A ALA* 3.6 23.8 - - - -
284A LEU* 4.2 9.2 - - + +
288A SER* 4.5 4.2 - - - +
289A SER* 3.6 34.6 + - - +
292A ALA* 3.7 10.8 - - + -
293A LEU* 3.5 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL 3.0 12.5 + - - +
123A GLY 3.6 8.3 - - - +
124A GLU 3.2 0.2 - - - -
125A MET* 1.3 74.5 - - - +
127A LYS* 1.3 65.7 + - - +
129A ALA* 3.1 10.6 + - - +
131A VAL* 3.1 28.9 + - + +
133A VAL* 3.8 26.9 - - + -
153A LEU* 3.9 17.5 - - + -
284A LEU* 3.9 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLY 3.0 21.5 + - - +
124A GLU* 2.9 38.7 + - - +
126A ALA* 1.3 75.4 - - - +
128A ALA* 1.3 59.1 + - - +
130A GLY* 3.0 19.8 + - - -
131A VAL 4.3 6.7 - - - +
133A VAL* 3.8 19.5 - - + -
135A VAL* 4.5 12.9 - - - +
----------------------------------------------------------
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 GLU 3.0 17.2 + - - +
125A MET 3.6 3.4 - - - +
126A ALA 3.2 0.2 - - - -
127A LYS* 1.3 76.6 - - - +
129A ALA* 1.3 58.1 + - - +
130A GLY 3.3 1.2 + - - -
288A SER* 3.5 35.4 - - - +
291A LYS* 5.2 6.1 - - + -
292A ALA* 4.4 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A MET 3.2 9.4 + - - +
126A ALA 3.1 11.4 + - - +
128A ALA* 1.3 76.8 - - - +
130A GLY* 1.3 59.8 + - - +
131A VAL* 3.5 15.4 + - + +
284A LEU* 4.4 2.5 - - + -
285A PRO* 3.7 24.4 - - + +
288A SER* 3.7 18.4 - - - +
----------------------------------------------------------
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