Contacts of the helix formed by residues 128 - 144 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 3.0 22.7 + - + +
127A ASN* 1.3 77.7 - - - +
129A LYS* 1.3 65.3 + - - +
130A GLY 3.2 0.7 - - - -
131A THR* 3.2 4.9 + - - -
132A PHE* 3.0 21.3 + - - +
171A ALA 4.5 2.7 - - - +
172A SER* 3.7 21.5 - - - +
175A GLY* 3.5 35.0 - - - +
176A VAL* 3.6 7.0 - - - +
179A LEU* 3.9 13.5 - - + -
120D TRP* 3.7 15.9 - - + -
124D ILE* 4.3 8.3 - - + -
128D LEU* 3.8 29.2 - - + -
171D ALA* 4.1 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER 3.9 17.3 + - - +
124A ILE* 2.7 15.8 + - + +
125A ALA* 3.3 21.3 - - + +
128A LEU* 1.3 74.8 - - - +
130A GLY* 1.3 57.8 + - - +
132A PHE* 3.3 1.4 + - - +
133A LEU* 3.0 43.0 + - + +
117D GLU* 2.9 33.6 + - - -
120D TRP* 3.4 30.7 - - + +
121D ASP* 3.1 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 3.2 31.0 - - - +
125A ALA 2.6 16.1 + - - -
126A VAL 3.2 15.4 + - - -
128A LEU 3.2 0.8 - - - -
129A LYS* 1.3 75.5 - - - +
131A THR* 1.3 60.0 + - - +
133A LEU 3.5 0.2 + - - -
134A VAL* 3.2 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A SER* 4.4 18.0 + - - -
104A ALA 4.9 4.7 + - - -
126A VAL 3.8 1.5 + - - -
127A ASN* 2.5 28.2 + - - -
128A LEU 3.2 5.0 + - - -
130A GLY* 1.3 73.9 - - - +
132A PHE* 1.3 54.6 + - - +
134A VAL* 3.3 1.9 + - - +
135A THR* 2.6 42.8 + - - +
153A ASN* 3.4 39.5 - - + +
154A ILE 5.7 0.7 + - - -
173A LYS* 5.9 0.2 + - - -
176A VAL* 3.9 16.5 - - + +
179A LEU* 4.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU 3.0 5.6 + - - +
129A LYS 3.6 7.9 - - - +
131A THR* 1.3 77.1 - - - +
133A LEU* 1.3 68.4 + - + +
135A THR* 3.2 3.8 + - - -
136A GLN* 2.7 60.9 + - - +
179A LEU* 3.5 21.5 - - + +
112D LEU* 3.5 24.7 - - + -
115D MET* 3.7 35.9 - - + -
116D SER 5.0 2.9 - - - -
117D GLU* 5.5 2.9 - - - -
120D TRP* 3.6 50.3 - + + -
167D THR* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL 3.2 22.0 - - - +
77A SER 3.3 20.2 - - - +
78A GLU 3.6 1.3 - - - -
79A ALA* 3.5 37.9 - - + +
82A ALA* 3.7 16.6 - - + +
129A LYS* 3.0 30.9 + - + +
130A GLY 3.9 0.2 - - - +
132A PHE* 1.3 93.5 - - + +
134A VAL* 1.3 58.6 + - - +
136A GLN* 3.9 10.5 - - - +
137A ALA* 3.0 31.0 + - - +
117D GLU* 5.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.9 7.4 - - + -
17A THR* 4.1 17.0 - - + +
76A VAL* 3.7 28.3 - - + -
82A ALA* 5.0 7.6 - - + +
85A LEU* 5.1 5.6 - - + -
86A LEU* 4.7 5.0 - - + +
100A VAL* 3.8 20.6 - - + -
102A SER* 3.4 21.8 - - - +
130A GLY 3.2 18.6 + - - +
131A THR* 3.7 3.4 - - - +
133A LEU* 1.3 73.6 - - - +
135A THR* 1.3 60.7 + - - +
137A ALA* 3.9 4.0 - - - +
138A ALA* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A SER* 4.9 0.6 + - - -
131A THR* 2.6 29.9 + - - +
132A PHE* 3.5 7.9 - - - -
134A VAL* 1.3 75.6 - - - +
136A GLN* 1.3 61.5 + - - +
138A ALA* 3.9 4.3 - - - +
139A ALA* 3.1 23.7 + - - +
151A ILE* 4.0 25.4 - - + +
153A ASN* 3.4 27.2 + - - +
179A LEU* 4.3 14.9 - - + +
183A ALA* 4.3 9.4 - - + -
194A CYS* 5.4 0.7 - - - -
112D LEU* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PHE* 2.7 40.4 + - + +
133A LEU* 3.9 11.7 - - - +
135A THR* 1.3 74.2 - - - +
137A ALA* 1.3 58.3 + - - +
139A ALA* 3.3 2.6 + - - +
140A GLN* 2.9 57.0 + - + +
112D LEU* 2.7 44.9 + - + +
113D LEU* 4.1 0.4 + - - +
114D HIS 4.3 0.4 - - - -
115D MET* 2.7 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA 4.2 9.4 - - - +
83A ARG* 4.3 15.9 - - + -
86A LEU* 3.5 29.1 - - + +
133A LEU 3.0 19.1 + - - +
134A VAL 4.1 0.4 - - - +
136A GLN* 1.3 77.5 - - - +
138A ALA* 1.3 60.4 + - - +
140A GLN* 3.6 14.9 + - - +
141A ALA* 3.2 23.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
86A LEU* 3.9 15.0 - - + +
97A PRO* 5.2 1.1 - - - +
100A VAL* 3.6 37.2 - - + -
134A VAL 2.9 19.5 + - - +
135A THR* 3.9 3.8 - - - +
137A ALA* 1.3 75.4 - - - +
139A ALA* 1.3 64.2 + - - +
141A ALA* 3.3 3.3 + - - +
142A LEU* 3.1 31.2 + - + +
151A ILE* 4.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR 3.1 18.6 + - - +
136A GLN 3.7 3.1 - - - +
138A ALA* 1.3 75.2 - - - +
140A GLN* 1.3 59.5 + - - +
142A LEU* 3.2 1.1 + - - +
143A VAL* 2.9 35.9 + - - +
151A ILE* 4.4 4.4 - - + +
187A LEU* 3.6 32.1 - - + -
192A ILE* 4.4 8.5 - - + -
112D LEU* 4.4 4.3 - - + -
113D LEU* 3.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 5.2 7.6 - - - +
136A GLN* 2.9 40.3 + - - +
137A ALA* 3.7 15.2 - - - +
139A ALA* 1.3 76.4 - - - +
141A ALA* 1.3 56.6 + - - +
143A VAL* 4.4 1.5 - - - +
144A SER* 2.6 36.6 + - - +
113D LEU* 2.5 48.8 + - + +
114D HIS* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.2 10.1 - - + -
90A GLN* 3.4 30.7 - - - +
96A PRO* 3.6 27.9 - - + +
97A PRO* 5.0 0.7 - - + -
137A ALA 3.2 16.9 + - - +
138A ALA 3.6 4.9 - - - +
139A ALA 3.2 0.4 - - - -
140A GLN* 1.3 76.7 - - - +
142A LEU* 1.3 64.6 + - - +
144A SER* 3.6 4.9 + - - -
145A ASN* 3.5 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PRO* 4.2 11.2 - - + +
97A PRO 3.3 28.3 - - - +
98A SER* 4.0 11.4 - - - +
100A VAL* 5.6 1.3 - - + -
138A ALA* 3.1 24.0 + - + +
139A ALA* 3.2 0.6 + - - -
141A ALA* 1.3 75.0 - - - +
143A VAL* 1.3 59.7 + - - +
145A ASN 3.1 2.9 + - - -
146A GLY 2.9 23.4 + - - -
147A CYS* 3.0 42.1 + - + +
148A ARG 4.2 1.1 - - - +
149A GLY* 3.8 24.7 - - - -
150A SER 4.8 0.4 - - - +
151A ILE* 5.0 6.5 - - + -
192A ILE* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA 2.9 21.3 + - - +
140A GLN* 4.4 2.5 - - - +
142A LEU* 1.3 75.4 - - - +
144A SER* 1.3 63.1 + - - +
145A ASN 3.1 1.3 + - - -
146A GLY* 3.2 12.4 + - - +
187A LEU* 4.5 1.3 - - + -
190A HIS* 3.6 49.8 - - + +
192A ILE* 3.7 14.4 - - + -
113D LEU* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN* 2.6 24.8 + - - +
141A ALA* 4.0 6.3 - - - -
142A LEU 3.2 0.4 - - - -
143A VAL* 1.3 79.2 - - - +
145A ASN* 1.3 71.5 + - - +
----------------------------------------------------------
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