Contacts of the helix formed by residues 129 - 144 (chain D) in PDB entry 6D6Q
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 129 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D THR* 4.1 17.0 - - - +
54D VAL* 5.8 3.1 - - + -
80D LEU* 6.0 1.8 - - + -
91D GLU* 5.3 4.7 - - - +
94D ARG* 3.3 32.8 - - - +
122D VAL* 3.8 39.7 - - + -
124D SER 4.2 1.6 - - - +
125D ASP* 4.2 23.3 - - - +
127D GLY* 3.1 3.6 - - - -
128D SER* 1.3 74.4 - - - +
130D LEU* 1.3 62.8 + - + +
132D CYS* 2.8 21.7 + - + +
133D CYS* 2.9 26.8 + - - -
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Residues in contact with LEU 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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80D LEU* 5.5 1.3 - - + -
94D ARG* 4.0 49.4 - - + +
97D LEU* 4.9 3.1 - - + -
98D ILE* 4.4 21.5 - - + -
129D LEU* 1.3 80.3 - - + +
131D ALA* 1.3 62.8 + - - +
132D CYS 2.9 0.2 - - - -
133D CYS* 4.2 8.5 - - + +
134D LEU* 2.9 36.7 + - + +
182D THR* 3.6 22.9 + - + +
194D MET* 4.4 9.9 - - + -
196D SER* 3.4 29.2 - - - +
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Residues in contact with ALA 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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49D GLN* 3.9 12.8 + - - +
128D SER* 3.5 15.3 + - - +
129D LEU 3.2 0.6 - - - -
130D LEU* 1.3 77.5 - - - +
132D CYS* 1.3 50.3 + - - +
134D LEU 4.5 0.7 - - - -
135D ASN* 2.4 36.7 + - - -
154D GLY* 3.1 30.7 - - - +
155D VAL* 3.7 18.4 - - - -
156D ALA* 4.1 7.0 - - + +
168D ASP* 6.3 0.7 - - - -
182D THR* 4.3 3.6 + - - +
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Residues in contact with CYS 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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47D PHE* 3.0 46.9 - - + -
48D LEU* 4.5 0.4 - - - -
49D GLN* 4.2 7.4 - - - +
52D THR* 4.2 21.5 - - + +
53D SER 4.4 0.7 - - - -
54D VAL* 3.2 33.4 - - + +
128D SER 3.3 9.5 + - - +
129D LEU* 2.8 11.1 + - + +
131D ALA* 1.3 79.3 - - - +
133D CYS* 1.3 64.1 + - - +
134D LEU 3.3 1.8 - - - -
135D ASN 3.4 1.0 + - - -
136D ALA* 3.0 19.4 + - - +
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Residues in contact with CYS 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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54D VAL* 3.8 28.5 - - - -
80D LEU* 4.1 20.6 - - - -
98D ILE* 4.4 9.9 - - + -
120D LEU* 4.2 18.1 - - + +
122D VAL* 4.9 3.4 - - - -
129D LEU* 2.9 35.2 + - - +
130D LEU* 3.1 10.3 + - + +
132D CYS* 1.3 76.7 - - - +
134D LEU* 1.3 58.6 + - - +
136D ALA* 3.4 1.2 + - - +
137D ALA* 2.9 31.0 + - - +
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Residues in contact with LEU 134 (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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98D ILE* 3.6 38.4 - - + -
101D THR* 5.1 4.9 - - + +
130D LEU* 2.9 25.4 + - + +
133D CYS* 1.3 76.6 - - - +
135D ASN* 1.3 63.0 + - - +
137D ALA* 3.2 3.2 + - - +
138D CYS* 2.9 20.1 + - - +
152D PHE* 3.4 31.3 - - + -
153D CYS 4.4 0.2 - - - +
154D GLY* 3.8 22.2 - - - +
182D THR* 4.9 2.5 - - + -
184D ALA* 3.7 30.3 - - + -
194D MET* 4.0 17.5 - - + -
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Residues in contact with ASN 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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47D PHE* 3.2 39.4 - - + -
49D GLN* 4.9 2.8 + - - -
131D ALA 2.4 26.4 + - - -
132D CYS 3.4 1.2 + - - -
133D CYS 3.4 0.2 - - - -
134D LEU* 1.3 76.2 - - - +
136D ALA* 1.3 58.0 + - - +
138D CYS* 3.3 3.9 + - - +
139D MET* 3.0 34.5 + - - +
152D PHE 5.1 0.2 - - - -
153D CYS* 3.1 24.0 - - - -
154D GLY 3.5 12.1 + - - -
220D VAL* 4.6 4.7 - - - +
224D TYR* 2.4 31.6 + - - +
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Residues in contact with ALA 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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45D ALA* 3.7 12.2 - - - +
47D PHE* 3.6 16.1 - - + +
54D VAL* 3.3 34.1 - - + -
56D ALA* 3.7 15.9 - - + +
120D LEU* 4.9 0.2 - - + -
132D CYS 3.0 7.7 + - - +
133D CYS 3.7 2.5 - - - +
135D ASN* 1.3 73.9 - - - +
137D ALA* 1.3 66.4 + - - +
139D MET* 3.3 3.8 + - - -
140D ALA* 2.9 24.8 + - - +
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Residues in contact with ALA 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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56D ALA* 4.2 9.5 - - - +
58D VAL* 4.9 0.2 - - - +
98D ILE* 4.6 13.5 - - + -
102D CYS* 4.9 4.7 - - - -
118D VAL* 4.3 20.0 - - + -
120D LEU* 4.6 3.4 - - + -
133D CYS 2.9 18.1 + - - +
134D LEU* 3.6 7.2 - - - +
136D ALA* 1.3 76.4 - - - +
138D CYS* 1.3 59.5 + - - +
140D ALA* 3.3 3.0 + - - +
141D LEU* 2.9 36.2 + - + +
152D PHE* 4.5 8.7 - - + -
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Residues in contact with CYS 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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134D LEU 2.9 13.4 + - - +
135D ASN* 3.6 8.5 - - - +
136D ALA 3.2 0.2 - - - -
137D ALA* 1.3 76.8 - - - +
139D MET* 1.3 71.1 + - + +
141D LEU* 3.3 7.0 + - - +
142D VAL* 2.9 26.3 + - - +
148D MET* 4.5 5.4 - - - -
151D LEU* 3.3 36.6 - - - -
152D PHE* 3.7 45.9 - - + +
224D TYR* 4.5 0.9 - - - +
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Residues in contact with MET 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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33D CYS* 4.0 19.1 - - + -
35D GLN* 2.8 42.3 + - - +
45D ALA* 3.7 8.1 - - + -
47D PHE* 5.0 1.8 - - + -
135D ASN 3.0 21.0 + - - +
136D ALA 3.8 0.4 - - - +
138D CYS* 1.3 85.3 - - - +
140D ALA* 1.3 57.9 + - - +
142D VAL* 3.3 8.8 + - + +
143D ASP 2.9 16.5 + - - -
151D LEU* 4.5 6.5 - - + -
224D TYR* 3.3 60.8 - - + -
227D SER* 5.7 5.4 - - - -
228D LEU* 5.1 15.9 - - + -
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Residues in contact with ALA 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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43D GLY* 4.2 6.6 - - - +
44D SER 4.4 5.4 - - - +
45D ALA* 3.6 10.7 - - + +
56D ALA* 4.0 21.8 - - + +
58D VAL* 3.3 24.8 - - + +
136D ALA 2.9 17.8 + - - +
137D ALA* 3.6 2.9 - - - +
139D MET* 1.3 73.4 - - - +
141D LEU* 1.3 67.2 + - - +
143D ASP* 3.1 4.3 + - - +
144D ALA* 2.9 23.9 + - - +
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Residues in contact with LEU 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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58D VAL* 4.2 22.9 - - + -
76D LEU* 5.4 2.5 - - + -
102D CYS* 4.1 29.2 - - + -
105D VAL* 5.4 0.2 - - + -
106D VAL* 5.3 7.9 - - + -
116D ILE* 4.6 9.2 - - + -
118D VAL* 4.3 14.8 - - + -
137D ALA* 2.9 24.5 + - + +
138D CYS 3.6 4.0 - - - +
140D ALA* 1.3 75.3 - - - +
142D VAL* 1.3 65.5 + - - +
144D ALA* 3.4 5.7 + - - +
146D VAL* 3.0 46.5 + - + +
148D MET* 3.9 24.2 - - + -
152D PHE* 4.5 6.3 - - + -
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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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35D GLN* 4.9 1.1 - - - +
138D CYS 2.9 20.7 + - - +
139D MET* 3.3 15.9 - - + +
140D ALA 3.1 0.2 - - - -
141D LEU* 1.3 74.8 - - - +
143D ASP* 1.3 56.1 + - - +
145D GLY* 2.7 29.2 + - - -
146D VAL 5.2 0.4 - - - +
148D MET* 3.4 21.1 - - + -
151D LEU* 4.0 17.3 - - + -
228D LEU* 4.3 18.8 - - + -
30G PRO* 4.8 4.3 - - + -
83G CYS* 3.2 43.2 - - + +
105G GLN 5.6 0.2 - - - +
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Residues in contact with ASP 143 (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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35D GLN* 3.4 24.6 - - - +
36D ASN* 2.5 48.0 + - - +
42D ASP 3.9 2.4 - - - +
43D GLY* 3.2 20.6 - - - -
44D SER 3.5 12.6 + - - +
139D MET 2.9 6.8 + - - +
140D ALA 3.1 6.9 + - - +
142D VAL* 1.3 78.5 - - - +
144D ALA* 1.3 57.3 + - - +
145D GLY 3.2 4.2 + - - -
231D ARG* 3.5 10.3 + - - +
83G CYS* 5.7 0.9 - - - -
105G GLN 4.0 13.9 - - - +
106G GLN* 4.2 5.9 - - - +
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Residues in contact with ALA 144 (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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42D ASP* 4.3 10.8 - - + -
43D GLY* 3.9 21.2 - - - +
58D VAL* 4.2 20.2 - - + -
60D GLY* 5.4 4.5 - - - -
61D PRO* 5.9 2.9 - - - +
140D ALA 2.9 15.2 + - - +
141D LEU* 3.8 4.9 - - - +
142D VAL 3.1 0.4 - - - -
143D ASP* 1.3 75.5 - - - +
145D GLY* 1.3 64.7 + - - +
146D VAL* 3.3 6.7 + - + +
106G GLN* 3.0 14.1 - - - +
107G LYS 6.2 0.2 - - - +
108G ARG* 5.4 6.6 + - - +
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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
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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