Contacts of the helix formed by residues 134 - 150 (chain A) in PDB entry 5XTD
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 ASP 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A PHE* 4.5 11.2 - - + -
43A THR 4.0 14.4 - - - +
44A ASN 4.1 8.7 - - - +
45A LEU* 5.7 1.1 - - - -
51A TRP* 5.0 0.2 - - - -
59A ARG* 3.7 20.9 + - - +
130A ILE* 2.6 38.7 + - + +
131A LEU* 5.1 0.2 - - - -
133A HIS* 1.3 77.3 - - - +
135A PRO* 1.3 69.2 - - - +
136A HIS* 3.1 4.1 + - - +
137A LYS* 3.1 38.0 + - - +
138A LEU* 4.2 4.9 + - - +
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Residues in contact with PRO 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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51A TRP* 4.1 27.4 - - + +
130A ILE 3.7 0.8 - - - +
131A LEU* 3.3 27.1 - - + +
133A HIS 3.8 3.1 - - - -
134A ASP* 1.3 90.5 - - - +
136A HIS* 1.3 59.3 + - + +
138A LEU* 3.1 11.9 + - + +
139A LEU* 2.9 29.2 + - + +
168A ASN 5.6 0.2 - - - -
169A LEU* 3.6 31.4 - - + +
172A ALA* 4.1 21.8 - - + -
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Residues in contact with HIS 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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51A TRP 2.6 29.7 + - - -
52A ARG* 3.9 0.2 - - - -
53A LEU* 3.1 43.3 + - + +
56A SER* 3.7 31.4 - - - -
59A ARG* 4.0 9.4 - - - +
61A ASP* 4.7 2.7 - - - +
62A TRP* 5.4 8.5 + - + +
134A ASP* 3.1 2.8 - - - +
135A PRO* 1.3 78.9 - - + +
137A LYS* 1.3 61.0 + - + +
139A LEU* 2.9 31.9 + - - +
140A GLU* 2.9 22.0 + - + +
172A ALA* 3.7 27.2 - - + +
175A GLU* 4.1 1.8 - - - -
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Residues in contact with LYS 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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41A ILE* 4.5 17.0 - - - +
42A PHE* 4.8 9.0 - - + -
59A ARG* 5.4 1.1 - - - +
61A ASP* 3.3 43.2 + - + +
134A ASP* 3.1 32.6 + - - +
135A PRO 3.4 0.2 - - - -
136A HIS* 1.3 76.6 - - - +
138A LEU* 1.3 57.3 + - - +
140A GLU* 3.4 12.0 + - - +
141A GLY 2.9 21.0 + - - -
249A ALA* 3.7 19.3 - - + +
252A PRO* 3.9 2.4 - - - +
253A THR* 3.8 21.2 - - - +
256A ARG* 3.1 27.7 - - - +
239O LYS* 5.3 7.5 - - - +
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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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115A VAL* 4.7 4.9 - - + -
130A ILE* 5.9 3.6 - - + -
131A LEU* 3.5 31.4 - - + -
134A ASP* 4.2 5.3 + - - +
135A PRO* 3.1 15.4 + - + +
136A HIS 3.1 0.2 - - - -
137A LYS* 1.3 80.0 - - - +
139A LEU* 1.3 57.7 + - + +
141A GLY* 3.0 2.4 + - - -
142A CYS* 2.8 37.3 + - - -
156A ILE* 5.3 11.2 - - + -
169A LEU* 5.4 7.9 - - + -
245A VAL* 3.7 28.3 - - + +
248A VAL* 3.7 29.2 - - + -
249A ALA* 3.8 13.3 - - + +
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Residues in contact with LEU 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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62A TRP* 5.6 9.9 - - + -
135A PRO* 2.9 27.2 + - + +
136A HIS* 2.9 27.6 + - - +
138A LEU* 1.3 76.1 - - + +
140A GLU* 1.3 61.4 + - + +
142A CYS* 3.0 16.5 + - - +
143A LEU* 2.9 27.3 + - - +
156A ILE* 5.0 6.3 - - + -
169A LEU* 4.2 9.0 - - + -
172A ALA 4.4 11.2 - - - +
173A ILE* 3.7 37.2 - - + -
176A ALA* 4.7 9.2 - - + -
182A ILE* 5.8 6.9 - - + +
193A PHE* 4.6 2.9 - - - -
195A VAL* 5.1 8.7 - - + -
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Residues in contact with GLU 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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61A ASP* 2.8 48.1 - - - +
62A TRP* 3.2 40.8 + - + -
65A THR* 3.9 12.0 - - + +
136A HIS* 2.9 15.9 + - - +
137A LYS* 3.6 16.9 + - - +
139A LEU* 1.3 75.6 - - - +
141A GLY* 1.3 57.4 + - - +
143A LEU* 3.3 8.0 + - - +
144A VAL* 2.9 35.4 + - + +
252A PRO* 4.0 10.1 - - + -
256A ARG* 3.5 14.4 + - - -
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Residues in contact with GLY 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 LYS 2.9 11.6 + - - -
138A LEU 3.0 5.1 + - - -
140A GLU* 1.3 76.3 - - - +
142A CYS* 1.3 59.6 + - - +
144A VAL 4.5 0.2 - - - -
145A GLY* 2.9 24.8 + - - -
248A VAL* 3.1 38.0 - - - +
251A SER* 3.9 0.3 + - - -
252A PRO* 3.5 13.7 - - - +
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Residues in contact with CYS 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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113A LEU* 4.8 3.5 - - + +
115A VAL* 4.2 15.9 - - + -
138A LEU* 2.8 36.4 + - - -
139A LEU* 3.0 13.2 + - - +
141A GLY* 1.3 74.5 - - - +
143A LEU* 1.3 59.0 + - - +
146A GLY* 2.9 22.3 + - - +
154A ALA* 4.2 10.1 - - + +
156A ILE* 3.7 30.1 - - - -
193A PHE* 3.1 25.7 - - + -
195A VAL* 4.7 3.6 - - + -
248A VAL* 4.4 4.9 - - - -
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Residues in contact with LEU 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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62A TRP* 4.3 13.0 - - + -
65A THR* 4.7 7.9 - - - +
69A LEU* 3.7 34.5 - - + -
139A LEU 2.9 12.0 + - - +
140A GLU* 3.6 10.1 - - - +
141A GLY 3.2 0.4 - - - -
142A CYS* 1.3 76.3 - - - +
144A VAL* 1.3 65.2 + - + +
147A ARG* 2.9 29.3 + - - +
181A LEU 3.5 24.7 - - - +
182A ILE* 4.5 4.0 - - + -
186A ALA* 4.2 10.3 - - + +
187A CYS* 3.9 15.3 - - - -
191A TYR* 4.7 3.2 - - + -
193A PHE* 3.5 27.9 - - + -
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Residues in contact with VAL 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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65A THR* 5.5 4.9 - - + +
68A ILE* 4.4 23.1 - - + -
69A LEU* 5.1 2.9 - - + -
76A ILE* 4.6 7.6 - - + +
80A ILE* 5.9 1.6 - - + -
140A GLU* 2.9 22.8 + - + +
141A GLY 4.3 1.1 - - - +
143A LEU* 1.3 84.9 - - + +
145A GLY* 1.3 60.0 + - - +
147A ARG* 3.2 8.3 + - - +
148A ALA* 2.9 25.1 + - + +
251A SER* 4.8 2.5 - - - +
252A PRO* 3.6 25.4 - - + -
255A CYS* 3.6 33.2 - - + -
256A ARG* 5.0 4.9 - - - +
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Residues in contact with GLY 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A TRP* 4.6 19.1 - - - -
113A LEU* 3.5 11.3 - - - +
141A GLY 2.9 15.7 + - - -
144A VAL* 1.3 76.8 - - - +
146A GLY* 1.3 65.3 + - - +
148A ALA* 3.2 8.6 + - - +
149A MET* 3.1 29.3 + - - +
248A VAL* 5.0 0.7 - - - -
251A SER* 4.6 1.1 + - - -
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Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A LEU* 3.6 14.8 - - - +
142A CYS 2.9 22.9 + - - -
145A GLY* 1.3 78.0 - - - +
147A ARG* 1.3 58.7 + - - +
149A MET 3.4 0.9 + - - -
150A GLY 3.2 2.4 + - - -
151A ALA* 2.8 39.7 + - - +
153A ALA 4.9 0.7 - - - -
154A ALA* 5.8 0.2 - - - -
191A TYR* 3.1 7.1 + - - -
193A PHE* 4.6 5.2 - - - -
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Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.5 28.8 - - + +
71A LYS* 3.1 21.4 + - - +
72A GLY* 3.0 33.6 - - - +
73A PRO* 3.9 18.0 - - - +
76A ILE* 5.1 8.7 - - + -
143A LEU 2.9 19.6 + - - +
144A VAL 3.4 5.8 - - - +
145A GLY 3.2 0.2 - - - -
146A GLY* 1.3 76.0 - - - +
148A ALA* 1.3 58.3 + - - +
150A GLY* 2.9 20.6 + - - -
191A TYR* 3.6 44.1 + - + +
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Residues in contact with ALA 148 (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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73A PRO* 3.9 23.4 - - + +
76A ILE* 4.3 21.3 - - + -
77A LEU* 5.4 14.7 - - + +
80A ILE* 5.9 4.3 - - + -
99A TRP* 5.1 13.7 - - + +
102A MET 3.8 9.9 - - - +
103A ASN* 5.4 0.3 - - - -
144A VAL* 2.9 14.3 + - + +
145A GLY* 3.2 13.4 + - - +
147A ARG* 1.3 76.7 - - - +
149A MET* 1.3 64.2 + - + +
150A GLY 3.5 0.3 + - - -
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Residues in contact with MET 149 (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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98A LYS 4.8 0.2 - - - +
99A TRP* 3.4 57.2 - - + +
102A MET* 3.1 61.5 - - - +
111A LYS* 3.6 6.9 + - - -
113A LEU* 4.1 7.9 - - + -
145A GLY 3.1 14.9 + - - +
146A GLY 3.8 5.6 - - - +
147A ARG 3.1 0.2 - - - -
148A ALA* 1.3 78.5 - - + +
150A GLY* 1.3 61.7 + - - +
151A ALA* 4.0 9.4 - - + +
241A THR* 3.2 41.5 - - + +
242A VAL 5.3 0.4 - - - +
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Residues in contact with GLY 150 (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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111A LYS* 4.3 15.4 + - - +
147A ARG* 2.9 25.5 + - - -
148A ALA 3.2 1.0 + - - -
149A MET* 1.3 79.1 - - - +
151A ALA* 1.3 65.3 - - - +
152A ARG* 3.5 2.1 + - - -
191A TYR* 3.4 11.0 - - - -
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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
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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