Contacts of the helix formed by residues 131 - 146 (chain B) in PDB entry 5X2L
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 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B GLU* 2.8 7.8 + - - +
130B PRO* 1.3 75.5 - - - +
132B ASP* 1.3 63.4 + - - +
133B GLU* 3.2 16.9 + - - +
134B SER* 3.1 23.9 + - - -
135B ARG* 3.0 34.6 + - - +
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Residues in contact with ASP 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B HIS* 5.7 0.4 - - - -
131B SER* 1.3 72.8 - - - +
133B GLU* 1.3 71.4 + - - +
135B ARG* 3.4 23.5 + - - +
136B GLU* 3.2 25.5 + - - +
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLU* 4.1 24.1 - - + +
131B SER* 3.2 23.2 - - - +
132B ASP* 1.3 82.0 + - - +
134B SER* 1.3 63.3 + - - +
136B GLU* 3.4 4.1 + - - +
137B ASN* 3.3 21.5 + - - +
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B CYS* 3.4 5.1 - - - +
129B GLU* 2.9 46.6 + - - +
131B SER* 3.1 15.1 + - - -
133B GLU* 1.3 76.6 - - - +
135B ARG* 1.3 67.1 + - - +
137B ASN* 4.7 3.8 - - - +
138B VAL* 3.1 33.4 + - - +
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Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B HIS* 3.2 45.6 + - + +
105B VAL* 3.9 4.8 - - - +
107B PRO* 3.7 31.4 - - + +
128B CYS* 3.7 22.6 - - - -
130B PRO* 4.4 8.9 - - - +
131B SER* 3.0 45.8 + - - +
132B ASP* 3.4 24.1 + - - +
133B GLU 3.3 0.2 - - - -
134B SER* 1.3 77.5 - - - +
136B GLU* 1.3 58.4 + - - +
139B ALA* 3.2 27.2 + - - +
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B HIS* 3.4 26.3 + - + +
132B ASP 3.2 13.8 + - - +
133B GLU* 3.9 3.8 - - - +
134B SER 3.2 0.2 - - - -
135B ARG* 1.3 78.5 - - - +
137B ASN* 1.3 60.3 + - - +
139B ALA* 3.5 0.9 + - - +
140B LYS* 2.9 55.9 + - - +
150B MET* 3.8 12.9 - - - +
152B HIS* 5.1 9.7 - - - -
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 4.5 16.9 + - - +
133B GLU 3.3 14.3 + - - +
134B SER* 4.4 3.6 - - - +
136B GLU* 1.3 78.0 - - - +
138B VAL* 1.3 63.4 + - + +
140B LYS* 3.3 9.1 + - - +
141B ARG* 2.9 28.7 + - - +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B VAL* 3.7 16.4 - - + -
126B VAL* 3.9 10.3 - - + -
127B TYR 3.6 20.0 - - - +
128B CYS* 3.7 17.7 - - + -
134B SER* 3.1 24.6 + - - +
137B ASN* 1.3 78.3 - - + +
139B ALA* 1.3 63.7 + - - +
141B ARG* 3.2 29.1 + - - +
142B VAL* 2.9 28.1 + - - +
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B VAL* 3.7 10.1 - - + +
82B HIS* 3.8 7.2 - - + +
105B VAL* 3.7 19.9 - - + +
135B ARG 3.2 19.1 + - - +
136B GLU 3.7 2.0 - - - +
137B ASN 3.2 0.2 - - - -
138B VAL* 1.3 80.0 - - - +
140B LYS* 1.3 52.4 + - - +
142B VAL 3.5 0.2 + - - -
143B THR* 2.7 37.6 + - - -
150B MET* 3.6 29.6 - - + -
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLU* 2.9 38.1 + - - +
137B ASN* 3.6 12.8 - - - +
138B VAL 3.2 0.2 - - - -
139B ALA* 1.3 74.3 - - - +
141B ARG* 1.3 59.4 + - - +
143B THR* 3.3 8.6 + - + +
144B GLU* 2.9 46.4 + - - +
150B MET* 3.5 26.9 - - + -
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B VAL* 3.8 14.8 - - - +
127B TYR 4.9 1.8 + - - -
137B ASN* 2.9 16.5 + - - +
138B VAL* 3.2 36.7 + - - +
140B LYS* 1.3 77.2 - - - +
142B VAL* 1.3 68.8 + - - +
144B GLU* 3.2 8.5 + - - +
145B GLU* 2.8 66.0 + - + +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B VAL* 3.9 11.7 - - + -
103B TYR* 3.7 38.4 - - + -
105B VAL* 4.4 4.0 - - + -
126B VAL* 3.8 35.7 - - + -
138B VAL* 2.9 22.8 + - + +
139B ALA 3.8 4.3 - - - +
141B ARG* 1.3 86.4 - - - +
143B THR* 1.3 57.5 + - - +
145B GLU* 4.6 4.7 - - - -
146B THR* 2.7 43.1 + - + +
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Residues in contact with THR 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B VAL* 3.5 11.0 - - - +
139B ALA 2.7 22.8 + - - -
140B LYS* 3.4 11.9 - - + -
142B VAL* 1.3 77.7 - - - +
144B GLU* 1.3 59.5 + - + +
146B THR* 3.9 4.3 - - - -
147B GLU* 3.1 9.9 + - - -
148B GLY 3.0 53.3 + - - +
149B ILE* 3.8 9.0 - - - +
150B MET* 3.1 23.8 - - + +
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Residues in contact with GLU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LYS* 4.2 15.9 + - - -
228A PRO* 5.5 10.3 - - - +
246A LEU* 5.5 9.7 - - + +
140B LYS* 2.9 33.9 + - - +
141B ARG* 3.2 6.5 + - - +
143B THR* 1.3 77.4 - - + +
145B GLU* 1.3 66.2 + - + +
147B GLU* 3.8 7.9 + - - +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LYS* 5.3 3.3 + - - +
141B ARG* 2.8 58.7 + - + +
142B VAL* 4.0 4.8 - - - +
144B GLU* 1.3 77.7 - - + +
146B THR* 1.3 62.3 + - + +
147B GLU* 3.3 6.5 + - - +
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LYS* 3.6 16.5 - - - +
78B ALA* 3.8 18.2 - - - +
80B VAL* 4.5 1.6 - - - +
103B TYR* 3.6 32.3 - - + +
142B VAL* 2.7 28.0 + - + +
143B THR* 3.5 6.2 + - - -
145B GLU* 1.3 81.0 - - + +
147B GLU* 1.3 69.0 + - - +
148B GLY* 3.2 6.8 + - - -
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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