Contacts of the helix formed by residues 131 - 143 (chain A) in PDB entry 5A91
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LYS* 4.1 0.7 - - - -
105A TYR 3.8 4.0 - - - -
106A ASN* 3.1 11.4 - - - +
107A PRO* 4.3 5.4 - - + -
108A ILE* 2.9 16.4 + - + +
109A ALA* 2.8 29.1 + - - +
125A ALA* 3.1 21.2 + - + +
126A ALA* 3.8 3.7 + - - -
129A TYR 3.2 3.7 - - - -
130A SER* 1.3 75.6 - - - +
132A ASN* 1.3 57.0 + - - +
133A THR* 2.9 14.7 + - - -
134A ALA* 2.9 36.4 + - + +
135A MET* 3.0 26.0 + - - +
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Residues in contact with ASN 132 (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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70A SER* 4.3 0.9 + - - -
73A LYS* 2.6 33.5 + - - -
103A VAL* 3.5 18.8 - - + -
104A ASN* 2.7 31.5 + - - +
105A TYR* 2.9 26.2 + - - +
130A SER 3.2 2.2 + - - -
131A ASP* 1.3 70.1 - - - +
133A THR* 1.3 65.8 + - - +
135A MET* 3.4 3.5 + - - +
136A ASN* 3.0 27.7 + - - -
166A ALA* 3.4 18.0 - - + +
167A PRO* 4.1 7.3 - - - +
169A LEU* 6.0 0.2 - - - +
170A ASN* 4.7 7.7 + - - +
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Residues in contact with THR 133 (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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97A ILE* 4.7 7.0 - - + -
101A ASP* 2.9 43.1 + - + +
102A LEU* 3.4 5.4 - - + +
103A VAL* 3.7 3.5 + - - +
106A ASN* 3.3 20.8 + - - +
109A ALA* 3.6 20.9 - - + -
131A ASP* 2.9 9.3 + - - -
132A ASN* 1.3 77.8 - - - +
134A ALA* 1.3 57.9 + - - +
136A ASN* 3.1 6.8 + - + +
137A LYS* 2.9 37.3 + - + +
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Residues in contact with ALA 134 (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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109A ALA* 4.8 0.8 - - + +
117A MET* 5.4 0.2 - - + -
122A LEU* 3.4 44.8 - - + +
125A ALA* 3.9 5.4 - - + -
126A ALA* 3.7 10.5 - - - +
131A ASP* 2.9 24.7 + - + +
133A THR* 1.3 77.9 - - - +
135A MET* 1.3 62.4 + - - +
137A LYS* 3.2 3.5 + - - +
138A LEU* 3.0 28.4 + - - +
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Residues in contact with MET 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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72A SER* 3.5 30.1 - - - +
73A LYS* 3.7 43.7 - - + -
76A ALA* 3.5 24.2 - - + -
126A ALA* 4.0 6.8 - - + +
131A ASP 3.0 14.4 + - - +
132A ASN* 3.5 8.1 - - - +
133A THR 3.3 0.2 - - - -
134A ALA* 1.3 74.9 - - - +
136A ASN* 1.3 60.5 + - - +
138A LEU* 3.1 7.2 + - - +
139A ILE* 2.9 53.9 + - + +
162A LEU* 4.3 8.1 - - + -
166A ALA* 4.5 7.0 - - + -
169A LEU* 4.1 10.1 - - + -
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Residues in contact with ASN 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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101A ASP 5.3 1.2 + - - +
103A VAL* 4.1 18.0 - - - +
132A ASN 3.0 20.4 + - - +
133A THR* 3.1 7.2 + - + +
135A MET* 1.3 76.7 - - - +
137A LYS* 1.3 59.2 + - + +
139A ILE* 3.4 8.0 + - - +
140A ALA* 2.9 30.8 + - - +
165A THR* 3.4 17.4 + - + +
166A ALA* 2.9 47.4 + - - +
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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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95A VAL* 3.7 19.1 - - + +
96A GLU 3.2 19.7 + - - -
97A ILE* 4.0 10.5 - - + -
98A LYS* 6.0 0.6 - - - +
101A ASP* 2.9 45.1 + - - -
119A LEU* 4.9 2.8 - - - +
122A LEU* 3.9 26.9 - - + -
133A THR* 2.9 19.1 + - + +
134A ALA 3.2 7.2 + - - +
136A ASN* 1.3 74.4 - - + +
138A LEU* 1.3 61.0 + - - +
140A ALA* 3.8 7.6 - - + +
141A HIS* 2.9 30.0 + - - +
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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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73A LYS 5.1 0.7 - - - +
76A ALA* 4.3 12.1 - - + -
77A ALA* 4.0 24.2 - - + +
80A VAL* 3.9 25.7 - - + +
119A LEU* 4.2 15.3 - - + +
122A LEU* 4.1 10.1 - - + +
123A GLY* 4.1 22.9 - - - +
126A ALA* 3.9 24.2 - - + -
134A ALA 3.0 19.2 + - - +
135A MET* 3.5 8.5 - - - +
137A LYS* 1.3 76.9 - - - +
139A ILE* 1.3 61.8 + - - +
141A HIS* 3.3 6.1 + - - +
142A LEU* 3.0 30.1 + - - +
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Residues in contact with ILE 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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76A ALA* 4.5 1.3 - - + -
135A MET* 2.9 52.8 + - + +
136A ASN* 3.7 8.5 - - - +
138A LEU* 1.3 76.1 - - - +
140A ALA* 1.3 62.6 + - - +
142A LEU* 3.2 10.6 + - - +
143A GLY 3.0 5.7 + - - -
144A GLY* 2.9 51.1 + - - -
145A PRO* 3.4 13.9 - - + -
148A VAL* 4.4 6.3 - - + -
162A LEU* 4.0 17.3 - - + -
164A ARG 4.3 0.9 - - - +
165A THR* 4.1 30.1 - - + -
166A ALA 4.9 0.2 - - - +
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Residues in contact with ALA 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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136A ASN 2.9 18.1 + - - +
137A LYS* 3.8 10.1 - - + +
139A ILE* 1.3 76.7 - - - +
141A HIS* 1.3 65.1 + - - +
143A GLY* 3.1 13.2 + - - -
144A GLY* 4.7 2.9 - - - +
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Residues in contact with HIS 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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80A VAL* 4.2 14.4 - - + -
83A GLN* 2.9 33.7 + - - -
90A LEU* 3.7 27.6 - - + +
93A GLN* 4.4 14.2 + - - -
95A VAL* 6.1 1.3 - - + +
119A LEU* 3.9 25.7 - - + +
137A LYS 2.9 18.5 + - - +
138A LEU* 3.5 4.5 - - - +
140A ALA* 1.3 78.5 - - - +
142A LEU* 1.3 62.1 + - - +
143A GLY* 3.4 0.7 + - - -
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Residues in contact with LEU 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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76A ALA* 3.8 14.4 - - - +
79A ALA* 3.7 33.2 - - + +
80A VAL* 3.8 12.6 - - + -
83A GLN* 3.6 38.2 + - + +
138A LEU 3.0 21.7 + - - +
139A ILE* 3.2 7.1 + - - +
141A HIS* 1.3 75.7 - - - +
143A GLY* 1.3 57.3 + - - +
144A GLY 4.7 1.3 - - - +
147A LYS* 3.2 30.3 - - + +
148A VAL* 3.8 23.1 - - + -
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Residues in contact with GLY 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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139A ILE 3.0 2.2 + - - -
140A ALA* 3.1 13.2 + - - -
141A HIS 3.2 0.9 - - - -
142A LEU* 1.3 78.6 - - - +
144A GLY* 1.3 58.5 + - - +
146A ASP* 3.8 1.9 - - - +
147A LYS* 3.2 27.0 + - - -
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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