Contacts of the strand formed by residues 148 - 161 (chain B) in PDB entry 1G13
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 LYS 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B VAL* 6.3 1.0 - - - +
144B SER* 3.2 3.2 - - - -
145B SER* 2.8 58.6 + - - +
146B SER* 3.2 4.5 - - - +
147B GLY* 1.3 77.5 - - - +
149B ARG* 1.3 63.4 + - - +
150B LEU* 3.4 18.2 + - + +
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Residues in contact with ARG 149 (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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9B ASP* 5.6 4.6 + - - -
13B ASP* 4.1 20.1 - - - +
14B PRO* 4.2 9.7 - - - +
140B GLU* 5.2 3.8 + - - -
142B VAL* 3.6 44.0 - - + +
143B LEU 3.8 3.8 - - - +
144B SER* 4.1 4.0 - - - -
147B GLY 3.7 3.6 + - - -
148B LYS* 1.3 72.5 - - - +
150B LEU* 1.3 64.7 + - - +
151B GLY 4.6 5.2 - - - +
152B CYS* 4.6 11.3 - - + +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASP* 4.0 1.3 - - - -
14B PRO* 3.3 16.4 - - + +
15B ALA* 2.8 32.7 + - - +
43B VAL* 4.0 25.6 - - + -
44B PRO 5.2 2.0 - - - +
45B LEU* 3.9 22.7 - - + -
46B SER 5.8 0.2 - - - +
49B LEU* 3.9 17.3 - - + -
143B LEU* 2.6 25.0 + - + +
144B SER* 3.9 4.5 - - - -
145B SER* 3.7 24.7 - - - +
148B LYS* 3.7 30.1 - - + +
149B ARG* 1.3 76.1 - - - +
151B GLY* 1.3 54.3 + - - +
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Residues in contact with GLY 151 (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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13B ASP* 3.9 10.0 - - - +
15B ALA* 3.4 18.2 - - - -
141B SER 4.5 0.7 - - - -
142B VAL* 3.5 3.5 - - - +
143B LEU* 2.8 35.6 + - - +
149B ARG* 3.8 2.4 - - - +
150B LEU* 1.3 80.4 - - - +
152B CYS* 1.3 62.6 - - - +
153B ILE* 5.6 0.2 - - - -
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Residues in contact with CYS 152 (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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7B ASN* 3.3 9.4 - - - +
8B CYS* 2.1 68.5 + - + -
9B ASP* 4.6 3.4 + - - +
13B ASP* 3.8 14.1 + - - +
15B ALA 4.5 3.0 + - - -
140B GLU* 4.0 11.4 - - - -
141B SER 3.3 5.6 - - - -
142B VAL* 3.6 26.2 - - + -
149B ARG* 4.6 13.0 - - - +
151B GLY* 1.3 74.2 - - - +
153B ILE* 1.3 67.7 + - - +
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TRP* 5.5 2.0 - - + -
6B ASP 3.4 10.1 - - - +
7B ASN* 3.6 14.4 - - - +
8B CYS* 3.7 0.9 - - - -
15B ALA 5.8 0.9 - - - +
16B VAL* 5.4 1.1 - - - -
17B ILE* 3.6 37.7 - - + +
20B LEU* 5.7 1.8 - - + -
139B ILE 4.0 0.3 - - - +
140B GLU* 3.3 4.5 - - - +
141B SER* 2.9 48.4 + - - +
152B CYS* 1.3 83.5 - - - +
154B LYS* 1.3 65.7 - - - +
155B ILE* 4.1 27.8 - - + -
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Residues in contact with LYS 154 (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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5B TRP* 3.2 5.5 - - - +
6B ASP* 2.9 37.2 + - + +
8B CYS* 3.7 24.7 - - + +
139B ILE 3.3 5.4 - - - +
140B GLU* 3.2 34.6 + - + -
153B ILE* 1.3 78.7 - - - +
155B ILE* 1.3 61.9 + - - +
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Residues in contact with ILE 155 (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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3B PHE* 3.8 19.7 - - + -
4B SER 3.6 11.0 - - - +
5B TRP* 4.1 3.1 - - + -
20B LEU* 3.7 27.8 - - + -
22B LEU* 5.3 2.7 - - + -
138B ARG* 3.3 5.5 - - - +
139B ILE* 2.8 53.6 + - + +
153B ILE* 4.1 23.6 - - + -
154B LYS* 1.3 80.2 - - - +
156B ALA* 1.3 68.4 + - - +
157B ALA* 4.2 6.9 + - + +
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Residues in contact with ALA 156 (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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2B SER 4.2 12.1 - - - +
3B PHE* 3.2 11.2 - - - -
4B SER* 2.9 36.2 + - - +
5B TRP* 4.9 0.2 - - - +
63B TRP* 6.0 1.1 - - + -
137B TYR 3.4 9.9 - - - +
138B ARG* 4.4 13.9 - - + +
155B ILE* 1.3 73.3 - - - +
157B ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 157 (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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2B SER 4.9 0.9 - - - -
3B PHE* 4.3 10.1 - - + +
22B LEU* 4.2 24.7 - - + -
27B ILE* 4.4 11.0 - - + -
136B ASN* 3.8 0.4 - - - -
137B TYR* 2.8 40.7 + - + +
155B ILE* 4.2 5.8 - - + -
156B ALA* 1.3 76.2 - - - +
158B SER* 1.3 63.6 + - - +
159B LEU* 5.5 2.7 - - + -
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Residues in contact with SER 158 (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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1B SER* 3.8 18.7 - - - -
2B SER* 4.6 1.9 + - - -
3B PHE* 5.5 0.6 - - - +
25B ASP* 4.5 10.3 + - - -
26B PRO* 3.6 18.2 - - - +
27B ILE* 2.8 30.6 + - - +
135B GLY 3.3 5.4 - - - -
136B ASN* 2.6 27.7 + - - -
157B ALA* 1.3 77.1 - - - +
159B LEU* 1.3 63.8 + - - +
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Residues in contact with LEU 159 (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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26B PRO* 4.4 1.7 - - - +
27B ILE* 3.3 32.3 - - + +
29B VAL* 4.5 13.7 - - + -
123B VAL* 6.1 2.7 - - + -
126B LEU* 4.3 23.3 - - + -
133B THR* 3.7 18.8 - - - +
134B THR* 3.4 3.9 - - - +
135B GLY 2.9 29.8 + - - +
137B TYR* 3.6 31.0 - - + +
157B ALA* 5.5 2.7 - - + -
158B SER* 1.3 82.0 - - - +
160B LYS* 1.3 65.5 + - - +
161B GLY 4.0 0.4 - - - -
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Residues in contact with LYS 160 (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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26B PRO* 3.7 26.2 - - + +
27B ILE 2.7 14.0 + - - +
28B ILE* 3.4 22.4 - - + +
29B VAL* 3.1 24.4 + - - -
134B THR* 4.0 13.1 - - + +
159B LEU* 1.3 77.6 - - - +
161B GLY* 1.3 62.4 + - - +
162B ILE* 3.5 4.6 + - - +
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Residues in contact with GLY 161 (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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29B VAL* 3.6 11.9 - - - +
130B SER* 2.7 31.0 - - - -
133B THR* 3.9 12.6 - - - -
134B THR* 2.8 23.3 + - - +
159B LEU 4.0 0.4 - - - -
160B LYS* 1.3 72.5 - - - +
162B ILE* 1.3 62.6 + - - +
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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