Contacts of the helix formed by residues 127 - 146 (chain A) in PDB entry 1CM8
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 GLU 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLY* 1.3 69.7 - - - +
128A ASP* 1.3 68.2 + - - +
130A ILE* 3.5 7.9 + - + +
131A GLN* 3.1 23.9 + - - +
279A ASN 5.0 9.1 - - - +
281A SER* 4.2 23.3 + - - +
310A TYR* 4.3 3.3 + - - -
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Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLY 3.1 1.2 + - - -
127A GLU* 1.3 83.1 - - - +
129A ARG* 1.3 63.5 + - - +
131A GLN* 3.4 16.4 + - - +
132A PHE* 3.1 23.1 + - - +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.7 31.1 - - - +
123A GLU* 3.4 25.8 + - - -
124A LYS 5.6 0.2 - - - -
125A LEU* 3.7 37.9 - - + +
126A GLY 2.9 9.0 + - - +
128A ASP* 1.3 76.4 - - - +
130A ILE* 1.3 65.9 + - - +
131A GLN 3.2 0.3 + - - -
132A PHE* 3.2 7.2 + - - +
133A LEU* 2.9 31.1 + - + +
163A GLU 5.7 2.0 + - - -
165A CYS* 3.6 35.7 - - - -
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Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 3.4 25.1 - - + +
126A GLY 2.9 38.2 + - - +
127A GLU* 3.9 7.0 - - + +
129A ARG* 1.3 71.3 - - - +
131A GLN* 1.3 60.8 + - - +
133A LEU* 3.6 0.9 + - - +
134A VAL* 2.9 41.9 + - + +
216A MET* 4.7 3.8 - - + -
219A MET* 3.9 38.1 - - + +
220A ILE* 4.1 27.1 - - + -
310A TYR* 4.0 11.9 - - - +
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Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU 3.1 12.9 + - - +
128A ASP* 3.5 21.1 + - - +
129A ARG 3.1 0.6 - - - -
130A ILE* 1.3 74.9 - - - +
132A PHE* 1.3 59.3 + - - +
134A VAL* 3.3 1.6 + - - -
135A TYR* 2.9 28.2 + - - +
310A TYR* 2.7 55.8 + - + +
311A PHE* 3.9 9.5 - - + -
312A GLU 4.5 0.2 + - - -
313A SER* 3.4 24.2 + - - -
314A LEU* 3.7 25.4 - - + +
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Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP 3.1 10.0 + - - +
129A ARG* 3.2 9.8 + - - +
131A GLN* 1.3 80.4 - - - +
133A LEU* 1.3 64.6 + - + +
135A TYR* 3.3 9.5 + + - +
136A GLN* 3.0 60.4 + - + +
164A ASP 4.3 8.1 - - - -
165A CYS* 3.5 26.2 - - + -
166A GLU* 4.9 4.9 - - + -
314A LEU* 4.2 27.6 - - + -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 3.6 18.6 - - + -
119A LEU* 4.8 5.2 - - + -
125A LEU* 4.1 17.3 - - + -
129A ARG* 2.9 21.2 + - + +
130A ILE 3.9 0.2 - - - +
132A PHE* 1.3 77.7 - - + +
134A VAL* 1.3 57.4 + - - +
136A GLN* 3.1 11.9 + - - +
137A MET* 3.0 31.9 + - + +
161A VAL* 3.9 24.5 - - + -
165A CYS* 3.6 32.8 - - + +
167A LEU* 3.9 8.9 - - + +
219A MET* 3.4 32.1 - - + -
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ILE* 2.9 20.9 + - + +
131A GLN* 3.9 2.9 - - - +
133A LEU* 1.3 70.5 - - - +
135A TYR* 1.3 65.8 + - - +
137A MET* 3.2 10.5 + - + +
138A LEU* 3.1 30.8 + - + +
212A VAL* 4.3 15.7 - - + -
216A MET* 3.5 39.3 - - + -
219A MET* 3.8 18.4 - - - -
291A MET* 5.0 0.7 - - + -
310A TYR* 5.0 0.7 - - + -
311A PHE* 3.9 21.1 - - + -
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Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLN 2.9 17.7 + - - +
132A PHE* 3.4 15.5 - + - +
134A VAL* 1.3 74.4 - - - +
136A GLN* 1.3 61.5 + - + +
138A LEU* 3.2 5.7 + - - +
139A LYS* 3.0 58.3 + - + +
142A ARG* 5.5 1.4 + - - -
306A LEU* 3.4 33.0 - - + -
311A PHE* 3.7 30.9 - + + -
314A LEU* 3.5 51.4 + - + -
315A HIS* 4.2 8.1 - - - -
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASN* 3.3 36.1 + - - +
132A PHE* 3.0 46.7 + - + +
133A LEU* 3.1 11.5 + - - +
135A TYR* 1.3 77.9 - - + +
137A MET* 1.3 66.5 + - - +
139A LYS* 4.4 5.8 - - - +
140A GLY* 3.1 17.8 + - - -
165A CYS 2.8 28.5 + - - -
166A GLU* 3.6 6.1 - - - +
167A LEU* 3.0 31.7 + - + +
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Residues in contact with MET 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.1 8.7 - - + -
133A LEU 3.0 34.3 + - - +
134A VAL* 3.2 16.8 + - - +
136A GLN* 1.3 77.1 - - - +
138A LEU* 1.3 56.5 + - + +
140A GLY 3.3 0.3 + - - -
141A LEU* 2.8 34.3 + - - +
154A LEU* 6.4 0.9 - - + -
159A LEU* 3.8 29.2 - - + -
167A LEU* 3.9 24.1 - - + +
169A ILE* 3.6 10.6 - - + +
212A VAL* 4.5 25.1 - - + +
215A ILE* 4.4 12.3 - - + -
216A MET 5.5 0.4 - - - -
219A MET* 3.9 26.0 - - + -
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL* 3.1 14.5 + - + +
135A TYR 3.5 3.6 - - - +
137A MET* 1.3 73.8 - - - +
139A LYS* 1.3 60.7 + - - +
140A GLY 3.2 1.1 - - - -
141A LEU* 3.5 8.9 - - + +
142A ARG* 2.7 30.3 + - - +
209A ILE* 4.1 18.6 - - + -
212A VAL* 4.1 22.9 - - + -
291A MET* 4.8 6.3 - - - -
302A ALA* 4.0 7.1 - - - +
305A ALA* 3.7 26.7 - - + -
306A LEU* 3.5 21.2 - - + +
311A PHE* 3.5 36.8 - - + -
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Residues in contact with LYS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A HIS* 3.8 14.7 + - + +
84A GLU* 6.1 2.2 - - - +
85A ASN* 3.7 21.4 + - - +
135A TYR* 3.0 54.5 + - + +
136A GLN* 3.4 4.9 + - - +
138A LEU* 1.3 74.5 - - - +
140A GLY* 1.3 64.0 + - - +
142A ARG* 3.3 17.1 + - - +
143A TYR* 3.0 23.2 + - - +
306A LEU* 3.9 21.8 - - + -
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Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A HIS* 4.2 3.4 - - - -
85A ASN* 3.7 24.1 - - - +
86A VAL* 4.1 6.4 - - - +
136A GLN 3.1 9.5 + - - -
137A MET 3.6 4.0 - - - -
139A LYS* 1.3 77.4 - - - +
141A LEU* 1.3 56.3 + - - +
143A TYR* 3.2 5.2 + - - +
144A ILE* 3.0 37.5 + - - +
169A ILE* 4.0 7.4 - - - -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A MET 2.8 17.4 + - - +
138A LEU* 3.5 8.5 - - + +
139A LYS 3.2 0.2 - - - -
140A GLY* 1.3 73.8 - - - +
142A ARG* 1.3 65.2 + - - +
144A ILE* 3.1 18.1 + - + +
145A HIS* 2.8 55.6 + - + +
151A HIS* 5.0 1.3 - - + -
154A LEU* 3.9 16.2 - - + -
169A ILE* 3.9 1.7 - - + +
208A ASP* 3.8 32.3 - - + +
209A ILE* 3.7 29.6 - - + -
212A VAL* 3.9 11.0 - - + -
302A ALA* 4.0 7.2 - - + -
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TYR* 5.5 2.0 + - - -
138A LEU 2.7 20.6 + - - +
139A LYS* 3.7 23.2 - - - +
141A LEU* 1.3 71.6 - - - +
143A TYR* 1.3 58.1 + - - +
145A HIS* 4.0 2.8 - - - +
146A ALA* 2.9 37.2 + - + +
302A ALA* 3.6 11.6 - - + +
303A GLY* 4.0 23.6 - - - +
306A LEU* 3.1 28.6 - - + +
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A HIS* 4.3 9.4 + - - -
81A MET* 3.4 25.0 - - + -
82A ARG* 2.9 43.6 + - - +
83A HIS* 3.5 41.3 - + + -
86A VAL* 4.2 7.6 - - + -
139A LYS 3.0 6.7 + - - +
140A GLY 3.4 7.6 - - - +
142A ARG* 1.3 73.8 - - - +
144A ILE* 1.3 72.8 + - + +
145A HIS 3.0 0.2 + - - -
146A ALA* 3.2 5.1 + - - +
147A ALA* 3.0 31.3 + - + +
323A VAL* 3.4 34.7 - - + +
324A GLN 5.3 1.7 + - - -
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Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A MET* 4.3 4.9 - - - -
86A VAL* 4.0 14.6 - - + -
140A GLY 3.0 16.6 + - - +
141A LEU* 3.6 13.7 - - + +
143A TYR* 1.3 80.0 - - + +
145A HIS* 1.3 62.3 + - + +
147A ALA* 3.5 6.9 - - - +
149A ILE* 2.9 64.7 + - + +
150A ILE 4.5 0.2 - - - +
151A HIS* 4.7 10.5 - - + +
169A ILE* 3.7 24.7 - - + -
172A PHE* 3.7 33.0 - - + -
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Residues in contact with HIS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 2.8 43.3 + - + +
142A ARG* 4.0 4.3 - - - +
144A ILE* 1.3 74.8 - - + +
146A ALA* 1.3 54.7 + - - +
147A ALA 2.9 4.9 - - - -
148A GLY* 2.6 25.8 + - - -
149A ILE 3.1 17.9 - - - -
150A ILE* 4.5 0.2 - - - -
205A GLN* 3.1 55.6 + - + +
208A ASP* 2.9 28.1 + - + -
209A ILE* 4.9 5.4 - - + -
302A ALA* 4.3 13.3 + - + +
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ARG* 2.9 28.5 + - + +
143A TYR 3.8 1.6 - - - +
145A HIS* 1.3 74.0 - - - +
147A ALA* 1.3 57.5 + - - +
148A GLY 3.2 2.8 + - - -
323A VAL* 3.3 29.3 - - + +
325A LYS* 3.9 14.0 - - - +
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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
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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