Contacts of the helix formed by residues 128 - 146 (chain D) in PDB entry 4CQM
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 LEU 128 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A TRP* 3.7 18.6 - - + -
124A ILE* 4.2 8.5 - - + -
128A LEU* 3.8 29.6 - - + -
171A ALA* 4.2 5.6 - - + +
124D ILE* 3.0 27.9 + - + +
127D ASN* 1.3 77.1 - - - +
129D LYS* 1.3 66.8 + - - +
130D GLY 3.3 0.9 - - - -
131D THR* 3.2 4.7 + - - -
132D PHE* 3.1 21.3 + - - +
172D SER* 3.6 17.7 - - - +
175D GLY* 3.4 33.0 - - - -
176D VAL* 3.5 6.7 - - - +
179D LEU* 3.6 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 2.9 35.6 + - - -
120A TRP* 3.5 29.8 - - + +
121A ASP* 3.3 30.1 + - - +
77D SER 4.2 14.6 + - - +
79D ALA 5.3 0.4 - - - +
124D ILE* 2.8 16.0 + - + +
125D ALA* 3.4 18.8 - - + +
128D LEU* 1.3 74.0 - - - +
130D GLY* 1.3 57.6 + - - +
132D PHE* 3.1 2.3 + - + +
133D LEU* 2.8 56.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL* 3.2 28.8 - - - +
125D ALA 2.9 13.5 + - - -
126D VAL 3.3 14.7 + - - -
128D LEU 3.3 1.0 - - - -
129D LYS* 1.3 75.7 - - - +
131D THR* 1.3 60.4 + - - +
133D LEU* 3.4 1.7 + - - +
134D VAL* 3.1 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D SER* 4.3 19.6 + - - +
104D ALA 4.9 5.2 + - - -
126D VAL 3.8 1.3 + - - -
127D ASN* 2.6 27.0 + - - -
128D LEU 3.2 4.6 + - - -
130D GLY* 1.3 72.7 - - - +
132D PHE* 1.3 58.8 + - - +
134D VAL* 3.4 2.2 + - - +
135D THR* 2.6 39.4 + - - +
153D ASN* 3.5 40.2 - - + +
154D ILE 5.7 0.7 + - - -
173D LYS* 5.7 0.9 + - - -
176D VAL* 4.0 15.9 - - + +
179D LEU* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.6 26.0 - - + -
115A MET* 3.8 31.4 - - + -
116A SER 5.0 1.6 - - - -
117A GLU* 5.5 2.9 - - - -
120A TRP* 3.7 46.7 - + + -
167A THR* 3.6 25.6 - - + -
128D LEU 3.1 13.0 + - - +
129D LYS 3.4 9.4 - - - +
131D THR* 1.3 78.0 - - - +
133D LEU* 1.3 72.2 + - + +
135D THR* 3.7 1.1 - - - -
136D GLN* 2.8 54.0 + - - +
179D LEU* 4.1 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 5.3 4.5 - - + -
76D VAL 3.3 20.6 - - - +
77D SER 4.0 4.5 - - - +
78D GLU 3.5 22.7 - - - -
79D ALA* 3.5 24.5 - - + +
82D ALA* 3.6 15.4 - - + +
129D LYS* 2.8 40.1 + - + +
130D GLY 3.7 3.6 - - - +
131D THR 3.3 0.2 - - - -
132D PHE* 1.3 94.8 - - + +
134D VAL* 1.3 55.5 + - - +
136D GLN* 3.9 9.7 - - - +
137D ALA* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 4.8 9.2 - - + -
17D THR* 4.2 18.6 - - + +
76D VAL* 3.9 26.5 - - + -
82D ALA* 4.8 9.6 - - + +
85D LEU* 5.0 4.9 - - + -
86D LEU* 4.4 3.9 - - + +
100D VAL* 3.8 24.9 - - + -
102D SER* 3.9 15.3 - - - +
130D GLY 3.1 17.7 + - - +
131D THR* 3.9 2.7 - - - +
133D LEU* 1.3 73.8 - - - +
135D THR* 1.3 61.3 + - - +
137D ALA* 3.4 4.2 + - - +
138D ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.3 15.9 - - + -
100D VAL* 5.6 0.7 - - - -
102D SER* 4.7 1.0 + - - -
131D THR* 2.6 28.8 + - - +
132D PHE* 3.7 6.3 - - - -
134D VAL* 1.3 77.7 - - - +
136D GLN* 1.3 56.6 + - - +
138D ALA* 3.9 4.3 - - - +
139D ALA* 2.9 31.0 + - - +
151D ILE* 3.9 30.7 - - + +
153D ASN* 3.4 22.2 + - - +
179D LEU* 4.2 9.9 - - + +
183D ALA* 4.4 11.9 - - + -
194D CYS* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 2.7 46.6 + - + +
113A LEU* 4.2 0.5 - - - +
114A HIS 4.3 0.4 - - - -
115A MET* 2.6 36.8 + - - +
116A SER 5.7 0.2 - - - -
132D PHE* 2.8 35.8 + - + +
133D LEU* 3.9 11.9 - - - +
135D THR* 1.3 77.6 - - - +
137D ALA* 1.3 56.0 + - - +
139D ALA* 3.3 2.5 + - - +
140D GLN* 3.0 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ALA* 3.8 16.4 - - + +
83D ARG* 4.1 19.1 + - + +
86D LEU* 3.8 24.3 - - + +
133D LEU 3.0 18.8 + - - +
134D VAL 3.9 0.4 - - - +
136D GLN* 1.3 77.1 - - - +
138D ALA* 1.3 62.0 + - - +
140D GLN* 3.4 14.5 + - - +
141D ALA* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LEU* 3.8 18.1 - - + +
97D PRO* 5.2 1.6 - - - +
100D VAL* 3.5 38.1 - - + -
134D VAL 2.9 19.7 + - - +
135D THR* 3.9 3.8 - - - +
137D ALA* 1.3 74.0 - - - +
139D ALA* 1.3 65.9 + - - +
141D ALA* 3.3 3.3 + - - +
142D LEU* 3.1 29.9 + - + +
151D ILE* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.4 5.2 - - + -
113A LEU* 3.6 15.0 - - + -
135D THR 2.9 19.1 + - - +
136D GLN 3.3 4.7 + - - +
138D ALA* 1.3 77.5 - - - +
140D GLN* 1.3 62.3 + - - +
142D LEU* 3.5 1.5 + - - +
143D VAL* 3.1 31.2 + - - +
151D ILE* 4.4 3.8 - - + +
187D LEU* 3.6 30.7 - - + -
192D ILE* 4.4 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 2.9 47.4 + - + +
83D ARG* 2.7 47.0 + - - +
136D GLN* 3.0 36.4 + - - +
137D ALA* 3.6 8.8 - - - +
138D ALA 3.2 0.2 - - - -
139D ALA* 1.3 76.8 - - - +
141D ALA* 1.3 58.4 + - - +
143D VAL* 4.0 2.7 - - - +
144D SER* 2.9 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ARG* 4.8 3.5 - - - +
86D LEU* 4.3 8.5 - - + -
90D GLN* 3.4 30.1 - - - +
96D PRO* 3.6 19.0 - - + +
97D PRO* 5.0 0.4 - - + -
137D ALA 3.1 15.7 + - - +
138D ALA 3.3 6.3 + - - +
140D GLN* 1.3 77.1 - - - +
142D LEU* 1.3 58.9 + - - +
144D SER* 3.1 5.9 + - - -
145D ASN* 2.9 30.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PRO* 4.1 13.2 - - + +
97D PRO 3.3 32.3 - - - +
98D SER* 4.2 2.5 - - - +
100D VAL* 5.3 2.7 - - + -
138D ALA 3.1 22.9 + - - +
139D ALA 3.9 0.2 - - - +
141D ALA* 1.3 76.8 - - - +
143D VAL* 1.3 59.4 + - - +
145D ASN* 3.3 1.6 + - - -
146D GLY 2.8 8.0 + - - -
147D CYS* 2.8 46.9 + - + +
148D ARG 3.6 17.3 - - - +
149D GLY* 4.0 18.8 - - - -
150D SER 5.0 0.4 - - - +
151D ILE* 5.2 5.4 - - + -
192D ILE* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.8 26.7 - - + -
139D ALA 3.1 18.3 + - - +
140D GLN 4.1 2.2 - - - +
142D LEU* 1.3 75.0 - - - +
144D SER* 1.3 60.2 + - - +
146D GLY* 2.9 20.2 + - - +
147D CYS 5.2 0.7 - - - -
187D LEU* 4.7 1.6 - - + -
190D HIS* 3.8 48.7 - - + +
192D ILE* 4.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLN* 5.1 1.2 + - - -
140D GLN 2.9 20.0 + - - -
141D ALA* 3.1 7.4 + - - -
143D VAL* 1.3 78.3 - - - +
145D ASN* 1.3 78.3 + - - +
146D GLY 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLN* 4.4 9.8 + - - +
94D SER 5.7 0.6 + - - -
95D ARG* 5.0 1.6 - - - +
96D PRO* 3.3 24.9 - - + +
141D ALA 2.9 15.8 - - - +
142D LEU 3.3 2.1 + - - +
143D VAL 3.1 0.2 - - - -
144D SER* 1.3 93.8 + - - +
146D GLY* 1.3 64.2 + - - +
147D CYS* 3.4 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LEU 2.8 3.8 + - - -
143D VAL* 2.9 15.9 + - - -
144D SER 3.4 0.4 + - - -
145D ASN* 1.3 79.8 - - - +
147D CYS* 1.3 60.7 + - - +
148D ARG* 4.3 1.0 + - - +
190D HIS 6.0 0.7 - - - -
----------------------------------------------------------
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