Contacts of the helix formed by residues 130 - 146 (chain A) in PDB entry 5OQN
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A PRO* 4.1 8.7 - - - +
128A SER* 3.3 7.2 + - - +
129A PRO* 1.3 80.2 - - - +
131A LYS* 1.3 72.7 + - - +
132A ASN* 3.5 25.2 + - - +
133A VAL* 3.6 30.5 + - + +
134A ARG* 3.3 22.0 + - - -
473B LYS* 4.0 19.8 + - - +
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Residues in contact with LYS 131 (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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129A PRO 3.3 3.0 + - - -
130A ASP* 1.3 78.5 + - - +
132A ASN* 1.3 77.1 + - - +
134A ARG* 3.3 25.3 + - - +
135A PHE* 3.0 28.5 + - + +
171A GLU* 2.7 40.6 + - + -
174A VAL* 4.2 3.9 - - + +
15C C 5.1 4.9 + - - -
16C A 3.8 31.0 + - - +
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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
----------------------------------------------------------
66A LEU 3.5 7.7 - - - +
67A PRO 3.4 26.5 + - - +
68A LEU 3.4 9.4 - - - +
69A LYS* 3.6 35.5 - - - +
70A LYS 4.5 2.8 + - - -
130A ASP* 3.3 12.6 + - - +
131A LYS* 1.3 93.9 - - - +
133A VAL* 1.3 65.7 + - - +
135A PHE* 3.2 7.5 + - - +
136A ARG* 3.1 22.3 + - - +
16C A 5.0 3.1 + - - -
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 4.0 8.6 - - + +
67A PRO* 3.9 19.1 - - + -
125A GLY* 3.6 20.0 - - - +
128A SER* 3.7 15.7 - - - +
130A ASP* 3.6 29.7 + - + +
131A LYS 3.4 0.2 - - - -
132A ASN* 1.3 77.1 - - - +
134A ARG* 1.3 62.6 + - - +
136A ARG* 4.0 0.3 - - - -
137A VAL* 3.1 34.0 + - + +
473B LYS* 4.7 2.2 - - - +
474B VAL* 3.4 39.5 - - + +
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Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY 3.9 5.6 - - - +
126A VAL 3.3 26.2 - - - +
127A GLU* 4.3 0.2 - - - +
128A SER 2.9 34.9 + - - +
129A PRO 3.5 3.4 + - - -
130A ASP 3.3 4.2 + - - +
131A LYS* 3.3 31.9 - - - +
132A ASN 3.3 0.6 - - - -
133A VAL* 1.3 79.2 - - - +
135A PHE* 1.3 65.5 + - - +
137A VAL* 3.6 0.8 + - - +
138A LEU* 3.2 29.8 + - + +
166A ARG* 4.6 1.6 - - - +
169A ASP* 2.7 42.1 + - - -
170A ARG* 5.3 0.6 - - - +
171A GLU* 4.2 8.5 - - - +
174A VAL* 4.0 16.4 - - + +
483B ILE* 3.3 36.8 - - - +
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Residues in contact with PHE 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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70A LYS* 3.6 47.8 - - + -
131A LYS 3.0 17.2 + - - +
132A ASN* 3.2 6.9 + - - +
134A ARG* 1.3 77.4 - - - +
136A ARG* 1.3 81.1 + - + +
138A LEU* 3.1 7.8 + - - +
139A GLN* 2.8 55.7 + - - +
173A THR* 3.4 28.7 - - + -
174A VAL* 3.7 13.2 - - + +
177A GLN* 3.4 35.4 - - + -
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Residues in contact with ARG 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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65A ILE* 3.5 20.4 - - + -
66A LEU* 3.5 26.0 - - + +
68A LEU* 3.0 16.2 + - - +
69A LYS 2.6 29.8 + - - -
71A ASN 3.6 8.3 - - - +
72A GLU* 3.4 28.3 + - - +
75A GLY* 3.9 23.2 - - - -
76A ASP* 4.0 5.3 + - - +
79A VAL* 4.2 4.4 - - + +
132A ASN 3.1 13.1 + - - +
135A PHE* 1.3 86.3 - - + +
137A VAL* 1.3 59.7 + - - +
139A GLN* 2.8 42.6 + - - +
140A LEU* 2.9 34.3 + - + +
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Residues in contact with VAL 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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66A LEU* 3.7 27.4 - - + -
122A VAL* 2.9 37.1 - - + +
123A LEU* 4.8 0.9 - - - -
125A GLY* 3.6 16.8 - - - +
126A VAL* 4.3 16.6 - - + -
133A VAL* 3.1 20.7 + - + +
134A ARG 3.9 3.4 - - - +
136A ARG* 1.3 78.7 - - - +
138A LEU* 1.3 65.8 + - + +
139A GLN 3.3 0.5 + - - -
140A LEU* 3.3 11.8 + - - +
141A LEU* 3.3 26.9 + - + +
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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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126A VAL* 4.5 12.6 - - + +
134A ARG* 3.2 20.4 - - + +
135A PHE* 3.1 7.6 + - - +
137A VAL* 1.3 84.0 - - + +
139A GLN* 1.3 62.1 + - - +
141A LEU* 3.4 10.1 + - + -
142A ALA* 3.2 19.9 + - - +
163A LEU* 3.7 30.3 - - + -
166A ARG* 4.2 29.2 - - + -
174A VAL* 4.3 15.5 - - + +
177A GLN* 3.5 19.8 - - + +
178A ALA* 4.2 12.8 - - + -
181A CYS* 3.5 15.4 - - - -
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Residues in contact with GLN 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 ASP* 4.4 14.3 + - - +
79A VAL* 4.4 19.3 - - + +
80A LYS* 6.1 1.4 - - - +
135A PHE* 2.8 43.0 + - + +
136A ARG* 2.8 42.9 + - - +
137A VAL 3.1 0.4 - - - -
138A LEU* 1.3 76.0 - - - +
140A LEU* 1.3 67.1 + - + +
141A LEU 3.3 0.3 + - - -
142A ALA* 3.5 7.7 + - - +
143A VAL* 3.5 21.1 + - + +
177A GLN* 4.2 14.7 - - - +
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Residues in contact with LEU 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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62A VAL* 3.3 32.3 - - + -
65A ILE* 4.6 7.0 - - + -
66A LEU* 4.3 11.0 - - + -
79A VAL* 3.6 40.4 - - + -
82A VAL* 5.4 7.0 - - + -
118A PHE* 4.1 14.1 - - + -
122A VAL* 3.8 23.3 - - + -
136A ARG 2.9 20.7 + - - +
137A VAL 3.3 5.6 + - - +
139A GLN* 1.3 75.9 - - - +
141A LEU* 1.3 62.6 + - + +
143A VAL* 3.2 20.5 - - + +
144A ILE* 3.2 16.4 - - + +
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Residues in contact with LEU 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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118A PHE* 6.5 0.4 - - + -
119A ILE* 3.8 34.8 - - + -
122A VAL* 4.2 13.9 - - + -
123A LEU* 4.3 14.4 - - + -
126A VAL* 6.3 0.4 - - + -
137A VAL* 3.3 30.0 + - + +
138A LEU* 3.8 19.5 - - + +
139A GLN 3.2 0.8 - - - -
140A LEU* 1.3 75.6 - - - +
142A ALA* 1.3 66.7 + - - +
144A ILE* 3.3 6.9 + - + +
145A MET* 2.8 41.3 + - + +
159A LEU* 4.2 13.2 - - + -
163A LEU* 5.6 3.4 - - + -
181A CYS* 3.7 12.6 - - - -
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Residues in contact with ALA 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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138A LEU 3.2 11.2 + - - +
139A GLN 3.9 4.5 - - - +
140A LEU 3.4 0.2 - - - -
141A LEU* 1.3 79.7 - - - +
143A VAL* 1.3 65.1 + - + +
145A MET* 3.4 15.1 + - - +
146A ASP* 4.1 8.3 - - - +
177A GLN* 4.5 8.5 - - - +
180A PHE* 3.9 26.2 - - + -
181A CYS* 3.3 21.5 - - - +
184A LYS* 4.2 7.4 - - - -
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Residues in contact with VAL 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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79A VAL* 4.1 20.9 - - + +
80A LYS* 5.7 7.2 - - - +
83A ALA* 3.6 31.7 - - + +
139A GLN* 3.6 17.7 - - + +
140A LEU* 3.2 15.0 - - + +
142A ALA* 1.3 79.6 - - + +
144A ILE* 1.3 67.0 + - + +
145A MET 3.5 0.3 + - - -
146A ASP* 4.4 8.2 - - - +
147A ASN* 4.0 11.1 - - - +
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Residues in contact with ILE 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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82A VAL* 4.7 8.3 - - + +
83A ALA* 4.1 12.8 - - - +
86A ILE* 4.1 29.5 - - + +
115A VAL* 4.7 7.2 - - + -
118A PHE* 5.0 13.5 - - + -
119A ILE* 4.2 20.6 - - + -
140A LEU* 3.2 21.1 - - + +
141A LEU* 3.5 14.4 - - + +
143A VAL* 1.3 83.1 - - + +
145A MET* 1.3 66.5 + - + +
146A ASP 3.3 1.8 - - - -
147A ASN* 3.2 16.5 + - - +
148A ILE* 3.1 39.4 + - + +
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Residues in contact with MET 145 (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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141A LEU* 2.8 50.2 + - + +
142A ALA* 3.5 11.4 - - - +
143A VAL 3.3 2.2 - - - -
144A ILE* 1.3 78.0 - - + +
146A ASP* 1.3 63.6 + - - +
147A ASN 3.2 0.7 + - - -
148A ILE* 3.3 42.6 + - + +
149A GLY 5.1 0.2 + - - -
159A LEU* 4.8 10.3 - - + -
163A LEU* 5.8 1.6 - - + -
181A CYS* 4.2 15.7 - - + +
184A LYS* 3.5 34.2 - - + +
185A PHE* 3.8 25.8 - - + -
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Residues in contact with ASP 146 (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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90A GLU* 5.7 0.3 - - - +
142A ALA 4.1 6.2 - - - +
143A VAL* 4.4 5.3 + - - +
144A ILE 3.3 0.6 - - - -
145A MET* 1.3 77.2 - - - +
147A ASN* 1.3 71.3 + - - +
148A ILE 3.4 2.8 + - - -
149A GLY 4.5 3.8 + - - -
184A LYS* 3.4 41.5 + - - +
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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