Contacts of the helix formed by residues 126 - 142 (chain D) in PDB entry 1CCW
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 PRO 126 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ALA* 3.3 22.0 - - - +
96D ASP* 3.1 17.5 - - - +
99D THR* 3.7 4.3 - - - +
107D CYS* 3.9 22.9 - - + -
111D ILE* 3.8 14.4 - - + -
122D LEU* 3.9 8.3 - - + -
124D GLY 3.6 8.3 - - - +
125D PHE* 1.3 78.9 - - - +
127D GLY* 1.3 64.8 + - - +
128D VAL 3.3 2.9 - - - -
129D ASN* 3.1 6.8 + - + -
130D PHE* 3.0 42.4 + - + -
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Residues in contact with GLY 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ILE* 4.3 11.4 - - - +
99D THR* 4.4 2.2 + - - -
125D PHE* 2.9 32.8 + - - -
126D PRO* 1.3 71.8 - - - +
128D VAL* 1.3 57.0 + - - +
130D PHE 3.4 0.7 + - - -
131D GLY* 3.0 22.9 + - - -
135D CYS* 3.9 8.6 - - - -
158D LEU* 4.6 6.5 - - - -
161D ILE* 3.7 14.0 - - - +
162D ILE* 5.3 0.4 - - - -
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Residues in contact with VAL 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TRP* 4.0 13.9 - - + -
26D THR* 2.7 27.4 + - - +
99D THR* 4.2 6.8 - - + +
104D TYR* 3.6 41.5 - - + +
126D PRO 3.3 0.4 - - - -
127D GLY* 1.3 75.3 - - - +
129D ASN* 1.3 63.5 + - - +
131D GLY* 3.2 6.6 + - - -
157D LEU* 3.7 21.5 - - + -
158D LEU* 3.8 42.9 - - + +
161D ILE* 3.9 11.0 - - + -
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Residues in contact with ASN 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D TRP* 3.8 26.2 + - - +
26D THR* 3.7 10.7 - - - +
99D THR* 4.7 0.2 + - - -
104D TYR* 3.1 36.9 + - - +
107D CYS* 3.2 25.7 - - - +
108D GLU* 3.7 16.8 + - - +
111D ILE* 4.1 17.9 - - + +
126D PRO* 3.1 9.8 + - + +
128D VAL* 1.3 78.2 - - - +
130D PHE* 1.3 62.3 + - - +
131D GLY 3.4 0.3 + - - -
133D LYS* 5.4 3.5 + - - -
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Residues in contact with PHE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D THR* 4.7 0.7 - - - -
29D GLU* 5.0 0.2 - - - +
70D ALA 2.8 30.7 - - - -
71D LEU* 3.8 4.7 - - + -
72D LEU* 3.5 33.2 - - + -
111D ILE* 4.2 20.6 - - + -
125D PHE* 3.3 37.9 - + + -
126D PRO* 3.0 36.7 + - + +
127D GLY 4.0 3.4 - - - +
129D ASN* 1.3 78.0 - - - +
131D GLY* 1.3 58.9 + - - +
133D LYS* 3.8 16.4 + - - +
134D GLY* 3.0 28.8 + - - -
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Residues in contact with GLY 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D THR* 3.8 13.0 - - - -
29D GLU* 3.5 7.9 - - - -
127D GLY 3.0 9.3 + - - -
128D VAL 3.2 10.5 + - - -
129D ASN 3.2 2.4 - - - -
130D PHE* 1.3 77.3 - - - +
132D VAL* 1.3 67.8 + - - -
133D LYS 3.2 0.2 - - - -
135D CYS* 3.0 26.7 + - - -
161D ILE* 3.6 9.0 - - - -
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Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLU* 2.8 32.3 + - + +
30D VAL* 3.7 30.5 - - + -
131D GLY* 1.3 72.3 - - - -
133D LYS* 1.4 55.9 + - - +
135D CYS* 3.7 1.4 - - - +
136D ARG* 2.8 61.0 + - - +
161D ILE* 3.7 23.6 - - + +
164D ALA* 3.7 19.5 - - + +
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Residues in contact with LYS 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLU* 3.0 30.2 + - - +
72D LEU* 6.4 0.7 - - + -
129D ASN 5.4 2.4 + - - -
130D PHE* 3.8 13.9 + - - +
132D VAL* 1.4 77.3 - - - +
134D GLY* 1.3 65.9 + - - +
136D ARG* 3.5 6.6 + - - +
137D LYS* 2.8 54.1 + - - +
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Residues in contact with GLY 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LEU* 3.6 27.9 - - - +
125D PHE* 4.8 0.4 - - - -
130D PHE* 3.0 26.2 + - - -
133D LYS* 1.3 78.1 - - - +
135D CYS* 1.3 64.9 + - - +
137D LYS* 3.1 13.8 + - - +
138D VAL* 3.1 17.5 + - - +
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Residues in contact with CYS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D PHE* 4.2 7.6 - - - -
127D GLY* 3.9 16.8 - - - -
130D PHE* 4.8 0.4 - - - -
131D GLY 3.0 20.7 + - - +
132D VAL 3.8 3.4 - - - +
134D GLY* 1.3 78.3 - - - +
136D ARG* 1.3 59.6 + - - +
138D VAL* 3.3 2.5 + - - +
139D LEU 3.1 12.1 + - - -
161D ILE* 4.1 11.9 - - - +
162D ILE* 4.2 9.4 - - - -
165D GLY* 3.6 16.1 - - - +
167D TRP* 2.9 56.0 + - + +
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Residues in contact with ARG 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLU* 2.8 42.0 + - - -
35D ALA* 3.9 7.1 - - - +
38D TYR* 3.5 52.3 - - - +
132D VAL* 2.8 34.3 + - - +
133D LYS* 3.8 6.3 - - - +
135D CYS* 1.3 73.8 - - - +
137D LYS* 1.3 60.9 + - + +
139D LEU* 3.2 1.0 + - - +
140D GLU* 2.8 42.0 + - - +
164D ALA* 2.9 26.8 + - - +
165D GLY* 3.5 19.5 - - - +
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Residues in contact with LYS 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LEU* 4.2 21.8 - - + -
76D ILE* 3.8 9.8 - - + +
133D LYS* 2.8 53.9 + - - +
134D GLY 3.1 10.4 + - - +
136D ARG* 1.3 77.7 - - + +
138D VAL* 1.3 63.2 + - - +
140D GLU* 3.4 9.9 + - - +
141D ALA* 3.1 25.5 + - - +
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Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LEU* 3.7 19.5 - - + -
75D HIS* 3.9 15.0 - - + +
76D ILE* 4.0 13.9 - - + -
79D LEU* 3.6 30.5 - - + -
93D SER* 4.5 2.2 - - - +
125D PHE* 3.9 16.4 - - + -
134D GLY 3.1 14.0 + - - +
135D CYS* 3.5 8.3 - - - +
136D ARG 3.1 0.4 - - - -
137D LYS* 1.3 77.8 - - - +
139D LEU* 1.3 62.6 + - - +
141D ALA* 3.2 10.2 + - - +
142D VAL* 3.4 16.2 + - + +
146D LEU* 3.8 13.5 - - + -
167D TRP* 4.4 4.5 - - + -
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D TYR* 3.6 25.1 - - + +
42D ILE* 3.8 23.8 - - + -
46D LYS* 2.8 50.7 + - + +
135D CYS 3.1 13.5 + - - +
136D ARG 3.2 5.6 + - - +
138D VAL* 1.3 76.0 - - - +
140D GLU* 1.3 63.0 + - + +
142D VAL* 3.2 11.9 + - - +
144D LEU 4.5 6.3 - - - +
146D LEU* 3.6 27.5 - - + +
165D GLY 3.9 7.2 - - - +
166D GLY* 3.7 24.5 - - - +
167D TRP* 4.3 0.2 - - + -
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Residues in contact with GLU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D TYR* 2.6 37.7 + - - +
46D LYS* 4.1 6.3 + - - +
136D ARG* 2.8 31.7 + - - +
137D LYS* 4.0 9.4 - - - +
139D LEU* 1.3 74.8 - - + +
141D ALA* 1.3 58.3 + - - +
142D VAL 3.4 4.6 + - - +
143D ASN* 5.5 0.3 - - - +
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Residues in contact with ALA 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D ILE* 3.5 33.0 - - + -
80D ARG* 3.1 38.3 + - - +
83D GLN* 5.2 1.4 + - - -
137D LYS 3.1 17.1 + - - +
138D VAL 3.6 4.9 - - - +
139D LEU 3.2 0.8 - - - -
140D GLU* 1.3 79.1 - - - +
142D VAL* 1.3 57.5 + - + +
143D ASN* 5.1 2.1 - - - +
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LYS* 2.8 29.3 + - - -
76D ILE* 5.1 2.0 - - + +
79D LEU* 4.1 21.3 - - + -
80D ARG* 4.6 11.0 - - + +
83D GLN* 3.7 6.7 - - - +
91D LEU* 3.6 27.1 - - + -
138D VAL* 3.6 14.4 - - + +
139D LEU* 3.3 17.5 + - - +
140D GLU 4.1 1.7 - - - +
141D ALA* 1.3 83.5 - - + +
143D ASN* 1.3 66.4 + - - +
144D LEU 3.7 18.4 - - - +
146D LEU* 4.4 8.7 - - + -
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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
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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) + - + + + + + -
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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