Contacts of the helix formed by residues 125 - 136 (chain B) in PDB entry 5G49
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 GLN 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A SER* 4.9 1.1 - - - -
86A SER* 3.1 5.8 - - - -
121B ARG* 3.6 32.7 + - - +
123B THR* 3.5 25.2 + - + +
124B LEU* 1.3 77.2 - - - +
126B LYS* 1.3 62.1 + - - +
127B ASN* 3.1 21.7 - - - +
128B ASP* 2.9 32.0 + - - +
129B ILE 3.4 3.8 + - - -
1152B ACT 3.0 29.7 - - + +
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Residues in contact with LYS 126 (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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85A ASP* 4.3 21.8 - - + +
86A SER* 3.3 6.2 + - - +
89A THR* 3.2 34.1 + - + +
92A GLU* 5.3 4.6 + - - -
125B GLN* 1.3 72.3 - - - +
127B ASN* 1.3 58.0 + - - +
129B ILE* 3.1 10.4 + - - +
130B ALA* 2.9 25.0 + - - +
145B ILE 4.4 11.5 + - - -
146B VAL* 4.1 11.4 - - + -
147B PRO* 5.0 6.0 - - - +
148B ARG 3.3 24.7 - - - +
1152B ACT 2.6 23.2 + - - +
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Residues in contact with ASN 127 (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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115B HIS* 3.9 11.9 + - - -
119B ASN* 5.7 0.4 + - - -
121B ARG* 3.4 20.6 + - - +
125B GLN* 3.1 31.2 - - - +
126B LYS* 1.3 78.0 - - - +
128B ASP* 1.3 58.9 + - - +
130B ALA* 3.7 10.1 - - - +
131B ALA* 3.1 25.3 + - - +
148B ARG* 4.8 21.5 - - + +
1152B ACT 5.2 1.6 - - - +
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Residues in contact with ASP 128 (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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112B SER* 3.4 30.4 - - - +
115B HIS* 2.8 25.6 + - - +
116B THR* 2.9 23.3 + - - +
121B ARG* 2.7 43.6 + - - -
124B LEU* 4.5 0.9 - - + -
125B GLN* 2.9 24.8 + - - +
127B ASN* 1.3 75.9 - - - +
129B ILE* 1.3 65.4 + - - +
131B ALA* 3.3 3.3 + - - +
132B ALA 3.0 17.5 + - - -
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Residues in contact with ILE 129 (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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86A SER* 3.9 23.8 - - - +
89A THR* 3.9 30.3 - - + -
90A ILE* 3.6 35.4 - - + -
108B LEU* 4.3 13.5 - - + -
112B SER* 3.3 19.3 - - - +
124B LEU* 3.8 14.6 - - + -
125B GLN 3.8 3.8 - - - +
126B LYS* 3.1 8.2 + - - +
128B ASP* 1.3 74.8 - - - +
130B ALA* 1.3 63.3 + - - +
132B ALA* 3.2 2.8 + - - +
133B VAL* 2.9 24.2 + - + +
146B VAL* 4.1 13.2 - - + -
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Residues in contact with ALA 130 (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 LYS 2.9 12.6 + - - +
127B ASN* 3.7 9.2 - - - +
129B ILE* 1.3 77.0 - - - +
131B ALA* 1.3 60.8 + - - +
133B VAL* 3.4 3.9 + - - +
134B THR* 3.0 28.0 + - - -
146B VAL* 3.8 24.8 - - + +
147B PRO 4.3 2.9 - - - +
148B ARG* 3.6 33.4 - - + -
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Residues in contact with ALA 131 (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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115B HIS* 3.5 44.4 - - + +
127B ASN 3.1 12.5 + - - +
128B ASP 3.7 0.9 - - - +
129B ILE 3.3 0.2 - - - -
130B ALA* 1.3 76.7 - - - +
132B ALA* 1.3 62.7 + - - +
134B THR* 3.2 8.2 + - - -
135B ARG* 3.1 37.4 + - - +
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Residues in contact with ALA 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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108B LEU* 4.3 8.5 - - + -
111B ARG* 3.7 19.5 + - + +
112B SER* 3.6 32.5 - - - +
115B HIS* 5.4 0.6 - - - +
128B ASP 3.0 10.0 + - - +
129B ILE 3.2 7.2 + - - +
131B ALA* 1.3 76.1 - - - +
133B VAL* 1.3 61.8 + - - +
135B ARG* 3.5 6.1 + - - +
136B THR* 2.9 32.3 + - - -
139B PHE* 4.4 2.2 - - + -
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Residues in contact with VAL 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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108B LEU* 4.0 19.3 - - + -
129B ILE* 2.9 26.6 + - + +
130B ALA* 3.8 6.3 - - - +
131B ALA 3.2 0.2 - - - -
132B ALA* 1.3 76.1 - - - +
134B THR* 1.3 61.4 + - - +
135B ARG 3.6 0.2 + - - -
136B THR 3.6 14.9 - - - +
139B PHE* 3.4 27.6 - - + +
140B ASP* 4.5 2.1 + - - +
142B LEU* 3.8 24.5 - - + +
143B VAL* 3.6 35.5 - - + +
146B VAL* 4.6 10.5 - - + +
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Residues in contact with THR 134 (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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130B ALA* 3.0 18.5 + - - +
131B ALA* 3.2 8.7 + - - +
133B VAL* 1.3 80.3 - - - +
135B ARG* 1.3 65.0 + - + +
136B THR 5.1 0.7 - - - +
137B ASP* 5.5 1.0 - - - +
143B VAL* 5.0 12.5 - - - +
147B PRO 5.6 2.3 + - - -
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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
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111B ARG* 5.4 3.8 + - - +
114B ASN* 5.7 1.4 - - - +
115B HIS* 3.5 31.8 + - - +
118B GLU* 3.4 36.0 + - - -
131B ALA* 3.1 24.8 + - - +
132B ALA* 4.2 4.7 - - - +
133B VAL 3.4 0.2 - - - -
134B THR* 1.3 82.9 - - + +
136B THR* 1.3 65.2 + - - +
137B ASP* 3.6 10.8 + - - +
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Residues in contact with THR 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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111B ARG* 3.1 43.8 + - - +
132B ALA* 2.9 20.3 + - - -
133B VAL 3.6 6.8 - - - +
134B THR 3.6 0.6 - - - -
135B ARG* 1.3 77.2 - - - +
137B ASP* 1.3 68.1 + - - +
138B ILE* 3.6 26.0 - - + -
139B PHE* 2.9 38.7 + - + +
140B ASP* 3.6 1.6 + - - -
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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