Contacts of the strand formed by residues 148 - 159 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C PRO* 5.8 6.1 - - - -
43C VAL* 5.6 8.4 - - - +
144C SER* 3.2 3.4 - - - -
145C SER* 2.7 36.1 + - - +
146C SER 3.2 3.1 + - - +
147C GLY* 1.3 75.9 - - - +
149C ARG* 1.3 75.5 + - - +
150C LEU* 3.3 14.2 + - + +
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Residues in contact with ARG 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ASP* 5.1 4.2 + - - -
12C LYS* 5.3 8.3 - - - +
13C ASP* 3.5 29.2 + - - +
14C PRO* 4.0 11.6 - - - +
142C VAL* 3.3 39.1 - - - +
143C LEU 3.9 2.0 - - - -
144C SER* 4.2 5.3 - - - -
147C GLY 3.6 8.3 + - - -
148C LYS* 1.3 81.2 - - - +
150C LEU* 1.3 59.0 + - - +
151C GLY 3.6 14.6 - - - -
152C CYS* 4.3 10.9 - - - +
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ASP* 3.6 1.9 - - - +
14C PRO* 3.3 12.7 - - + +
15C ALA* 2.9 31.6 + - - +
43C VAL* 3.8 28.3 - - + -
44C PRO 4.8 3.4 - - - +
45C LEU* 3.9 18.6 - - + -
46C SER 5.6 0.2 - - - +
49C LEU* 3.5 32.3 - - + -
143C LEU* 2.7 25.1 + - + +
144C SER* 3.8 4.9 - - - -
145C SER* 3.7 20.0 - - - +
148C LYS* 3.3 21.1 + - + +
149C ARG* 1.3 77.0 - - - +
151C GLY* 1.3 55.0 + - - +
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Residues in contact with GLY 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ASP* 3.9 9.0 - - - -
15C ALA* 3.4 18.8 - - - -
141C SER 4.5 0.2 - - - -
142C VAL* 3.5 1.0 - - - -
143C LEU* 2.8 37.4 + - - +
149C ARG* 3.6 4.9 - - - +
150C LEU* 1.3 80.8 - - - +
152C CYS* 1.3 64.9 + - - +
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Residues in contact with CYS 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ASN* 3.3 9.4 + - - +
8C CYS* 2.0 70.9 + - + -
9C ASP* 4.6 2.2 + - - +
13C ASP* 3.9 13.7 + - - +
15C ALA 4.5 2.4 + - - -
140C GLU* 4.1 11.4 - - - -
141C SER 3.2 6.3 - - - -
142C VAL* 3.6 24.9 - - + -
149C ARG* 4.3 10.1 - - - +
151C GLY* 1.3 75.9 - - - +
153C ILE* 1.3 66.8 + - - +
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Residues in contact with ILE 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C TRP* 5.6 2.7 - - + -
6C ASP 3.4 9.0 - - - +
7C ASN* 3.6 19.5 - - - +
8C CYS* 3.9 0.4 - - - -
15C ALA 5.8 0.7 - - - +
16C VAL* 5.7 1.1 - - - -
17C ILE* 3.9 27.1 - - + +
20C LEU* 5.8 1.8 - - + -
139C ILE* 3.8 0.9 - - + +
140C GLU* 3.3 4.2 - - - +
141C SER* 2.8 52.7 + - - +
152C CYS* 1.3 83.3 - - - +
154C LYS* 1.3 65.4 + - - +
155C ILE* 4.2 23.1 - - + -
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Residues in contact with LYS 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C TRP* 3.1 4.7 - - - -
6C ASP* 2.9 39.8 + - + +
7C ASN 5.8 0.4 - - - +
8C CYS* 3.7 26.9 - - + +
139C ILE 3.3 6.3 - - - +
140C GLU* 3.7 29.6 - - + -
153C ILE* 1.3 78.5 - - - +
155C ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE* 3.7 24.9 - - + -
4C SER 3.4 4.3 - - - +
5C TRP* 4.0 12.3 - - + -
20C LEU* 3.7 19.5 - - + -
22C LEU* 5.4 3.1 - - + -
138C ARG* 3.1 4.2 - - - +
139C ILE* 2.7 56.4 + - + +
153C ILE* 4.2 24.2 - - + -
154C LYS* 1.3 82.5 - - - +
156C ALA* 1.3 67.0 + - - +
157C ALA* 4.7 5.6 - - + -
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Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C SER 3.9 9.4 - - - +
3C PHE* 3.1 9.7 - - - -
4C SER* 2.8 49.4 + - - +
63C TRP* 5.9 2.7 - - + -
137C TYR 3.4 9.4 - - - +
138C ARG* 4.1 7.9 - - + +
155C ILE* 1.3 74.1 - - - +
157C ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C SER 4.4 0.9 + - - -
3C PHE* 4.1 21.3 - - + +
22C LEU* 4.6 5.4 - - + -
27C ILE* 4.5 19.3 - - + -
136C ASN* 3.8 1.1 - - - +
137C TYR* 2.9 39.9 + - + +
155C ILE* 4.3 5.3 - - + -
156C ALA* 1.3 77.6 - - - +
158C SER* 1.3 63.5 + - - +
159C LEU* 5.4 2.7 - - + -
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Residues in contact with SER 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C SER 4.5 2.6 + - - -
2C SER* 3.9 18.4 - - - -
3C PHE 4.9 0.2 - - - +
25C ASP* 4.2 7.9 + - - -
26C PRO* 3.2 25.4 - - - +
27C ILE* 2.8 30.8 + - - +
135C GLY 3.4 6.7 - - - -
136C ASN* 3.0 23.6 + - - +
157C ALA* 1.3 75.7 - - - +
159C LEU* 1.3 61.8 + - - +
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Residues in contact with LEU 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PRO* 4.3 2.0 - - - +
27C ILE* 3.4 40.6 - - + +
29C VAL* 4.3 12.8 - - + -
132C LEU* 3.4 38.1 - - + -
133C THR 4.3 4.7 - - - +
134C THR* 3.2 5.4 - - - +
135C GLY 2.9 31.5 + - - +
137C TYR* 3.4 28.7 - - + +
157C ALA* 5.3 2.9 - - + +
158C SER* 1.3 77.9 - - - +
160C LYS* 1.3 61.1 + - - +
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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