Contacts of the helix formed by residues 134 - 150 (chain X) in PDB entry 5A31
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 SER 134 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107X LYS* 6.1 0.4 - - - +
132X LEU 3.2 5.0 + - - -
133X PRO* 1.3 72.0 - - - +
135X GLU* 1.3 68.4 + - - +
136X ILE* 3.6 20.7 + - - +
137X GLU* 2.5 45.3 + - - +
138X VAL* 3.1 15.7 + - - +
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Residues in contact with GLU 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77X TYR* 3.9 9.1 + - - -
104X LEU* 4.4 15.9 - - + -
107X LYS* 4.0 34.9 - - + +
108X LYS* 5.9 6.0 - - - +
133X PRO 3.5 3.2 + - - -
134X SER* 1.3 73.7 + - - +
136X ILE* 1.3 67.7 + - + +
138X VAL* 3.3 6.2 + - - +
139X LYS* 3.0 52.4 + - + +
166X GLN* 5.7 1.6 - - - +
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Residues in contact with ILE 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134X SER* 3.1 14.9 - - - +
135X GLU* 1.3 88.4 - - + +
137X GLU* 1.3 61.2 + - + +
139X LYS* 3.4 7.6 + - + +
140X TYR* 3.0 27.2 + - - +
162X ILE* 4.0 28.2 - - + +
166X GLN* 4.2 30.1 - - + +
167X ARG* 5.1 0.4 - - - -
168X THR* 4.2 14.4 - - + +
171X ILE* 3.6 30.8 - - + +
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Residues in contact with GLU 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133X PRO* 3.4 10.3 - - + +
134X SER* 2.5 44.4 + - - +
136X ILE* 1.3 77.7 - - + +
138X VAL* 1.3 61.5 + - + +
140X TYR* 3.3 10.1 + - - +
141X LYS* 3.0 34.9 + - + +
170X LYS* 5.1 13.5 - - - +
171X ILE* 5.8 0.7 - - - -
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Residues in contact with VAL 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77X TYR* 3.7 19.3 - - - +
81X VAL* 4.2 21.1 - - + -
100X TYR* 3.2 37.7 - - + +
103X ALA* 4.7 6.5 - - + -
104X LEU* 3.7 22.2 - - + -
133X PRO* 4.5 4.3 - - + -
134X SER 3.1 16.0 + - - +
135X GLU* 3.5 6.3 - - - +
137X GLU* 1.3 77.3 - - + +
139X LYS* 1.3 56.3 + - - +
141X LYS* 3.0 11.1 + - - +
142X LEU* 2.9 26.5 + - - +
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Residues in contact with LYS 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104X LEU* 4.2 23.8 - - + -
135X GLU* 3.0 43.1 + - + +
136X ILE* 3.6 5.8 - - + +
138X VAL* 1.3 72.8 - - - +
140X TYR* 1.3 66.0 - - - +
142X LEU* 3.2 9.2 - - - +
143X ALA* 3.0 22.5 + - - +
158X ILE* 3.7 37.8 + - + +
159X LEU* 4.4 2.4 - - + +
161X GLY* 4.4 6.5 + - - -
162X ILE* 3.6 39.4 - - + +
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Residues in contact with TYR 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X ILE 3.0 14.5 + - - +
137X GLU* 3.3 13.9 - - - +
139X LYS* 1.3 74.6 - - - +
141X LYS* 1.3 68.1 + - + +
143X ALA* 3.0 4.9 + - - +
144X GLU* 2.9 53.3 + - + +
159X LEU* 4.4 8.9 - - + +
170X LYS* 3.7 48.4 + - + +
171X ILE* 3.9 24.2 - - + -
173X MET* 5.7 3.5 - - - +
174X MET* 3.6 33.2 - - + +
48Y GLY 5.2 4.9 + - - -
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Residues in contact with LYS 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X ASP* 3.6 24.0 + - - +
88X PHE* 4.4 21.7 - - + -
100X TYR* 3.5 33.0 - - + +
137X GLU* 3.0 19.2 + - + +
138X VAL* 3.0 8.7 + - - +
140X TYR* 1.3 78.0 - - + +
142X LEU* 1.3 64.9 + - - +
144X GLU* 3.2 21.8 + - - +
145X CYS* 3.1 28.4 + - - -
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Residues in contact with LEU 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520H ARG* 4.8 2.0 - - - +
97X VAL* 3.5 31.8 - - + +
100X TYR* 3.0 36.7 - - + -
101X THR* 4.1 13.9 - - + +
104X LEU* 4.0 26.5 - - + -
138X VAL 2.9 9.8 + - - +
139X LYS* 3.2 11.9 - - - +
141X LYS* 1.3 75.6 - - - +
143X ALA* 1.3 59.1 + - - +
145X CYS* 3.1 7.2 + - - +
146X TYR* 2.9 37.0 + - + -
158X ILE* 4.3 26.2 - - + -
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Residues in contact with ALA 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139X LYS 3.0 9.4 + - - +
140X TYR 3.0 5.4 + - - +
142X LEU* 1.3 77.9 - - - +
144X GLU* 1.3 65.0 + - - +
146X TYR* 3.4 6.6 + - - +
147X THR* 2.9 28.6 + - - -
155X ALA* 3.9 15.8 - - + +
158X ILE* 5.1 2.7 - - + -
159X LEU* 3.9 21.8 - - + -
174X MET* 3.4 24.2 - - + -
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Residues in contact with GLU 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88X PHE* 3.6 29.8 - - + -
140X TYR* 2.9 48.7 + - + +
141X LYS* 3.5 22.2 - - - +
142X LEU 3.2 0.2 - - - -
143X ALA* 1.3 76.5 - - - +
145X CYS* 1.3 63.7 + - - +
147X THR* 3.2 9.5 + - - -
148X VAL* 3.0 28.6 + - + +
174X MET* 4.2 17.0 - - - -
89Y HIS* 5.8 4.2 - - - -
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Residues in contact with CYS 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88X PHE* 3.4 32.1 - - - -
93X TYR* 3.9 22.2 - - + +
96X ALA* 4.1 17.3 - - - -
97X VAL* 3.6 19.5 - - + -
100X TYR* 4.7 5.4 - - - -
141X LYS 3.1 21.0 + - - -
142X LEU* 3.5 7.0 - - - +
144X GLU* 1.3 76.7 - - - +
146X TYR* 1.3 62.6 + - - +
148X VAL* 3.2 4.4 + - - +
149X LEU* 3.0 28.0 + - - +
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Residues in contact with TYR 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520H ARG* 2.7 47.2 + - - -
94X ARG* 5.1 4.0 - - - -
97X VAL* 3.8 20.2 - - + -
142X LEU* 2.9 32.1 + - + -
143X ALA* 3.7 6.5 - - - +
144X GLU 3.3 0.2 - - - -
145X CYS* 1.3 75.1 - - - +
147X THR* 1.3 56.3 + - - +
149X LEU* 3.1 19.6 + - + +
150X LYS 2.9 22.7 + - - -
151X GLN* 3.1 29.0 + - + +
154X ASP* 3.1 48.2 - - + -
155X ALA* 4.0 8.1 - - + +
158X ILE* 4.1 22.8 - - + +
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Residues in contact with THR 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143X ALA 2.9 15.1 + - - -
144X GLU* 3.4 12.8 - - - -
146X TYR* 1.3 75.9 - - - +
148X VAL* 1.3 59.0 + - + +
150X LYS* 2.9 23.2 + - - +
151X GLN 5.1 2.0 - - - +
152X ASP* 5.0 7.2 - - - +
155X ALA* 4.1 10.2 - - - +
174X MET* 4.5 8.3 - - + -
178X LEU* 4.2 24.2 - - + +
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Residues in contact with VAL 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88X PHE* 5.5 2.2 - - + -
93X TYR* 3.2 54.1 - - + +
144X GLU* 3.0 20.6 + - + +
145X CYS 3.2 6.5 + - - +
147X THR* 1.3 76.9 - - + +
149X LEU* 1.3 62.3 + - + +
150X LYS* 3.3 16.8 + - - +
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Residues in contact with LEU 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93X TYR* 3.6 26.9 - - + -
94X ARG* 4.2 33.9 - - + +
97X VAL* 4.3 11.7 - - + -
145X CYS 3.0 20.7 + - - +
146X TYR* 3.4 23.1 - - + +
147X THR 3.1 0.4 - - - -
148X VAL* 1.3 76.9 - - - +
150X LYS* 1.3 72.5 + - - +
151X GLN* 3.5 30.1 + - - +
334Y ILE 5.3 0.9 - - - +
335Y SER* 6.4 0.4 - - - -
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Residues in contact with LYS 150 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146X TYR 2.9 0.6 + - - -
147X THR 2.9 16.9 + - - +
148X VAL 3.9 11.7 + - - +
149X LEU* 1.3 81.9 + - - +
151X GLN* 1.3 60.7 + - - +
152X ASP* 3.4 16.1 + - - +
367X GLN* 3.9 37.9 + - - +
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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