Contacts of the strand formed by residues 148 - 161 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A SER* 3.0 7.5 - - - -
145A SER* 2.9 38.8 + - - +
146A SER* 4.5 9.4 - - - +
147A GLY* 1.3 77.2 - - - +
149A ARG* 1.3 64.0 + - - +
150A LEU* 3.4 10.9 + - + +
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Residues in contact with ARG 149 (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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8A CYS* 4.8 4.2 - - - +
13A ASP* 3.7 23.9 + - - +
14A PRO* 4.0 12.1 - - - +
140A GLU* 5.0 3.2 + - - -
142A VAL* 3.6 38.3 - - - +
143A LEU 4.1 2.2 - - - -
144A SER* 4.3 3.1 - - - -
147A GLY 3.6 3.0 + - - +
148A LYS* 1.3 72.7 - - - +
150A LEU* 1.3 65.4 + - - +
151A GLY 4.4 1.8 - - - +
152A CYS* 3.4 34.6 - - - +
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Residues in contact with LEU 150 (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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13A ASP* 3.3 4.9 - - - +
14A PRO* 3.3 14.4 - - + +
15A ALA* 3.0 28.4 + - + -
43A VAL* 4.2 24.7 - - + -
44A PRO 5.4 1.6 - - - +
45A LEU* 4.0 18.6 - - + -
46A SER 5.7 0.2 - - - +
49A LEU* 3.6 31.4 - - + -
143A LEU* 2.8 26.8 + - + +
144A SER* 3.8 9.9 - - - -
145A SER* 3.8 18.8 - - - +
148A LYS* 4.0 11.7 - - + +
149A ARG* 1.3 79.8 - - - +
151A GLY* 1.3 56.8 + - - +
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Residues in contact with GLY 151 (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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13A ASP* 3.9 8.9 - - - +
15A ALA* 3.5 19.1 - - - -
141A SER 4.5 0.2 - - - -
142A VAL* 3.5 3.5 - - - +
143A LEU* 2.8 36.6 + - - +
149A ARG* 3.8 3.1 + - - +
150A LEU* 1.3 80.2 - - - +
152A CYS* 1.3 62.5 - - - +
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Residues in contact with CYS 152 (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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7A ASN* 3.3 11.6 + - - +
8A CYS* 2.1 67.9 + - + -
9A ASP 4.7 0.5 + - - -
13A ASP* 4.0 7.6 + - - +
15A ALA 4.6 2.0 + - - -
140A GLU* 3.9 13.7 - - - -
141A SER 3.2 7.2 - - - +
142A VAL* 3.8 15.0 - - + -
149A ARG* 3.4 29.4 - - - +
151A GLY* 1.3 77.8 - - - +
153A ILE* 1.3 62.8 + - - +
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Residues in contact with ILE 153 (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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5A TRP* 4.1 8.5 - - + -
6A ASP 3.3 17.0 - - - +
7A ASN* 4.7 2.2 - - - +
8A CYS* 3.8 3.4 - - - -
17A ILE* 3.9 29.2 - - + -
20A LEU* 3.9 18.4 - - + -
139A ILE 3.9 0.5 - - - +
140A GLU* 3.3 4.0 - - - +
141A SER* 2.9 48.0 + - - +
152A CYS* 1.3 76.7 - - - +
154A LYS* 1.3 69.5 + - - +
155A ILE* 3.8 27.1 - - + -
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Residues in contact with LYS 154 (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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5A TRP* 3.2 6.1 - - - +
6A ASP* 2.9 35.0 + - + +
8A CYS* 3.9 21.9 - - + +
139A ILE 3.3 5.2 - - - +
140A GLU* 3.0 40.4 + - + -
152A CYS* 4.7 0.2 - - - -
153A ILE* 1.3 78.1 - - - +
155A ILE* 1.3 62.9 + - - +
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Residues in contact with ILE 155 (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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3A PHE* 3.8 18.6 - - + -
4A SER 3.4 9.0 - - - +
5A TRP* 4.0 1.3 - - + -
20A LEU* 3.8 24.2 - - + -
22A LEU* 5.0 5.8 - - + -
138A ARG* 3.2 6.1 - - - +
139A ILE* 2.8 53.1 + - + +
153A ILE* 3.8 23.3 - - + -
154A LYS* 1.3 80.1 - - - +
156A ALA* 1.3 69.5 + - - +
157A ALA* 4.5 7.4 - - + +
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Residues in contact with ALA 156 (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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2A SER 4.2 9.4 - - - +
3A PHE* 3.2 10.0 - - - -
4A SER* 2.8 49.1 + - - +
63A TRP* 6.5 0.4 - - + -
137A TYR 3.5 9.0 - - - +
138A ARG* 4.3 5.2 - - + +
155A ILE* 1.3 73.7 - - - +
157A ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 157 (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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2A SER 4.9 1.3 - - - -
3A PHE* 4.5 10.3 - - + +
22A LEU* 4.3 24.0 - - + -
27A ILE* 4.5 10.8 - - + -
136A ASN* 3.8 0.5 - - - +
137A TYR* 2.8 40.0 + - + +
155A ILE* 4.2 6.2 - - + -
156A ALA* 1.3 75.3 - - - +
158A SER* 1.3 66.7 + - - +
159A LEU* 5.5 2.5 - - + -
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Residues in contact with SER 158 (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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1A SER* 2.6 31.6 + - - -
25A ASP* 4.8 4.4 + - - -
26A PRO* 3.4 16.6 - - - +
27A ILE* 2.8 27.4 + - - +
135A GLY 3.3 11.4 - - - -
136A ASN* 2.8 20.1 + - - -
157A ALA* 1.3 76.5 - - - +
159A LEU* 1.3 67.8 + - - +
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Residues in contact with LEU 159 (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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26A PRO* 4.3 2.8 - - - +
27A ILE* 3.2 33.2 - - + +
29A VAL* 4.5 19.3 - - + -
123A VAL* 5.8 4.3 - - + -
133A THR* 3.6 26.5 - - + +
134A THR* 3.3 3.8 - - - +
135A GLY 2.9 28.9 + - - +
137A TYR* 3.4 31.9 - - + +
157A ALA* 5.5 2.5 - - + -
158A SER* 1.3 84.2 - - - +
160A LYS* 1.3 61.6 + - - +
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Residues in contact with LYS 160 (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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26A PRO* 3.9 27.3 - - + +
27A ILE 2.8 8.8 + - - +
28A ILE* 3.2 19.9 - - + +
29A VAL* 2.9 24.6 + - - -
134A THR* 3.9 9.9 - - + -
159A LEU* 1.3 74.1 - - - +
161A GLY* 1.3 67.2 + - - +
162A ILE 3.6 15.6 + - - +
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Residues in contact with GLY 161 (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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29A VAL* 3.2 17.1 - - - +
130A SER* 3.5 23.6 - - - -
133A THR* 4.2 2.2 - - - -
134A THR* 2.9 16.1 + - - +
159A LEU 4.1 0.4 - - - -
160A LYS* 1.3 73.8 - - - +
162A ILE* 1.3 80.9 + - - +
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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