Contacts of the helix formed by residues 130 - 141 (chain I) in PDB entry 5A0Q
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 GLY 130 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1I THR* 4.1 0.2 - - - +
2I THR* 3.5 23.7 + - - +
128I GLY* 3.2 1.2 - - - -
129I SER* 1.3 75.9 - - - +
131I SER* 1.3 62.3 + - - +
132I LEU 3.3 3.0 + - - -
133I ALA* 3.4 9.3 + - - +
134I ALA* 3.0 22.7 + - - +
162I GLY* 4.5 2.8 - - - -
166I ASP* 3.0 22.0 + - - -
169I SER* 3.9 3.0 + - - -
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Residues in contact with SER 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H TYR* 4.1 9.3 + - - -
126I THR* 3.2 14.9 + - - -
127I MET* 3.6 29.1 + - - -
128I GLY 3.2 17.2 + - - -
129I SER 3.2 2.5 + - - -
130I GLY* 1.3 77.7 - - - +
132I LEU* 1.4 68.9 + - - +
134I ALA* 4.2 3.8 - - - -
135I MET* 2.9 26.7 + - - +
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Residues in contact with LEU 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H TYR* 3.3 56.7 - - + -
129I SER 5.5 4.9 - - - +
130I GLY 3.3 0.6 - - - -
131I SER* 1.4 80.5 + - - +
133I ALA* 1.3 64.0 + - - +
135I MET* 3.9 1.0 - - - +
136I ALA* 3.1 23.4 + - - +
144b TYR* 3.3 54.4 - - + +
145b LEU* 4.3 7.5 - - + +
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Residues in contact with ALA 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I GLY* 3.6 11.0 - - - +
132I LEU* 1.3 80.7 - - - +
134I ALA* 1.3 58.8 + - - +
136I ALA* 3.9 2.1 + - - +
137I VAL* 3.4 24.1 + - - +
161I ALA* 4.0 16.6 - - - +
162I GLY* 4.8 1.6 - - - -
165I ASN* 4.5 8.3 - - + -
166I ASP* 5.9 1.8 - - + +
144b TYR* 3.1 18.6 + - + +
148b PRO* 3.4 28.2 - - + +
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Residues in contact with ALA 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I THR* 3.9 19.1 - - + -
4I ALA* 5.7 0.2 - - + -
126I THR* 3.7 19.1 - - + -
130I GLY 3.0 17.4 + - - +
131I SER 3.8 2.7 - - - +
133I ALA* 1.3 76.9 - - - +
135I MET* 1.4 58.0 + - - +
137I VAL* 3.1 7.4 + - - +
138I PHE* 2.9 32.6 + - + -
158I ALA* 3.9 19.6 - - - +
161I ALA* 4.7 0.9 - - - -
162I GLY 5.2 0.9 - - - +
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Residues in contact with MET 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H TYR* 3.4 35.9 - - + +
26H ILE 5.6 2.5 - - - +
27H ALA* 5.7 4.5 - - - -
28H ASN 5.8 4.7 - - - +
29H ARG* 6.0 2.0 - - - -
114I TYR* 5.0 9.0 - - - +
122I LEU* 5.7 2.7 - - - -
124I TYR* 3.7 36.1 - - + +
125I VAL* 4.4 5.4 - - + -
126I THR* 3.2 47.5 + - + +
131I SER* 2.9 10.3 + - - +
132I LEU 4.2 1.1 - - - +
134I ALA* 1.4 74.1 - - - +
136I ALA* 1.3 59.2 + - - +
138I PHE* 4.2 4.7 - - + -
139I GLU* 2.8 30.0 + - - +
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Residues in contact with ALA 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I LEU 3.1 11.5 + - - +
133I ALA 4.1 4.9 - - - +
134I ALA 3.3 0.4 - - - -
135I MET* 1.3 75.5 - - - +
137I VAL* 1.4 55.9 + - - +
139I GLU* 3.6 9.5 - - - +
140I ASP* 3.0 30.3 + - - +
145b LEU* 2.9 55.1 - - + +
149b LEU* 3.6 12.2 - - + +
175b VAL* 4.4 0.7 - - - +
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Residues in contact with VAL 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I ALA 3.4 17.0 + - - +
134I ALA 3.1 7.0 + - - +
136I ALA* 1.4 71.1 - - - +
138I PHE* 1.4 60.4 + - - +
140I ASP* 4.4 0.4 - - - -
141I LYS* 3.0 41.8 + - + +
154I LEU* 5.6 2.0 - - + +
157I GLU* 5.0 7.0 - - + -
158I ALA* 4.2 22.9 - - + +
161I ALA* 3.7 17.9 - - + -
148b PRO* 4.0 6.7 - - + -
149b LEU* 3.8 10.5 - - + -
152b GLU* 3.4 25.4 - - + +
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Residues in contact with PHE 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I ALA* 3.6 20.4 - - + -
5I GLY 4.2 4.9 - - - -
6I VAL* 4.0 24.0 - - + -
124I TYR* 3.6 36.0 - - + -
125I VAL 4.8 0.2 - - - -
126I THR* 3.2 35.2 - - + -
134I ALA* 2.9 21.1 + - + -
135I MET* 3.4 6.0 + - - +
137I VAL* 1.4 74.5 - - - +
139I GLU* 1.3 59.3 + - - +
142I PHE* 2.9 33.7 + - + +
154I LEU* 3.8 26.7 - - + -
155I VAL* 4.0 14.8 - - + -
158I ALA* 3.3 24.5 - - + -
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Residues in contact with GLU 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H ARG* 4.3 20.8 + - - +
124I TYR* 3.7 27.6 + - + +
135I MET 2.8 18.1 + - - +
136I ALA* 3.6 5.4 - - - +
138I PHE* 1.3 77.7 - - - +
140I ASP* 1.3 63.3 + - - +
141I LYS 3.4 0.3 + - - -
142I PHE* 4.2 9.0 - - - +
145b LEU* 5.0 5.0 - - - +
174b ARG 4.6 1.7 - - - +
175b VAL* 3.3 45.8 - - + +
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Residues in contact with ASP 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I ALA 3.0 17.9 + - - +
137I VAL 3.4 3.6 + - - +
139I GLU* 1.3 77.3 - - - +
141I LYS* 1.3 78.4 + - + +
142I PHE 4.9 1.0 - - - +
149b LEU* 3.9 22.3 - - + +
152b GLU* 3.5 12.5 - - - +
171b ARG* 3.2 44.7 + - - +
172b CYS* 6.0 0.2 - - - -
174b ARG* 5.6 2.0 + - - +
175b VAL* 3.9 17.0 - - + +
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Residues in contact with LYS 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I VAL* 3.0 32.1 + - + +
140I ASP* 1.3 102.3 + - + +
142I PHE* 1.4 67.3 + - - +
143I ARG* 3.5 10.4 + - - +
154I LEU* 4.1 17.7 - - + +
152b GLU* 3.8 11.2 + - - +
171b ARG* 4.7 11.5 - - - +
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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