Contacts of the strand formed by residues 135 - 145 (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 GLY 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C LYS* 5.0 4.5 - - - -
58C GLU 5.9 1.3 - - - -
133C THR 3.3 1.9 + - - -
134C THR* 1.3 80.7 - - - +
136C ASN* 1.3 66.8 + - - -
137C TYR* 3.5 10.1 - - - -
158C SER* 3.4 2.9 - - - -
159C LEU 2.9 32.1 + - - +
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Residues in contact with ASN 136 (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* 5.3 8.2 + - - +
57C LYS* 3.6 4.7 - - - +
58C GLU* 2.8 75.2 + - + +
63C TRP* 4.1 7.0 - - + -
135C GLY* 1.3 76.0 - - - -
137C TYR* 1.3 62.3 + - - +
157C ALA 3.9 3.4 - - - +
158C SER* 3.0 22.7 + - - +
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Residues in contact with TYR 137 (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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55C LEU* 4.5 15.3 - - + -
56C GLU 3.3 16.8 - - - +
57C LYS* 3.3 31.2 - - + -
63C TRP* 3.8 5.9 - - - -
131C TRP* 3.1 31.2 + + - -
132C LEU* 3.6 2.7 - - + -
133C THR 2.5 44.7 + - - -
135C GLY 3.5 19.7 - - - -
136C ASN* 1.3 75.9 - - - +
138C ARG* 1.3 64.0 + - - +
156C ALA* 3.4 3.3 - - - +
157C ALA* 2.9 37.0 + - + +
159C LEU* 3.4 31.0 - - + -
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Residues in contact with ARG 138 (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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54C VAL 3.9 0.5 - - - +
55C LEU* 3.5 3.4 - - - +
56C GLU* 2.6 66.5 + - + +
63C TRP* 3.5 58.9 - - + +
137C TYR* 1.3 78.4 - - - +
139C ILE* 1.3 65.0 + - - +
155C ILE 3.1 12.3 - - - +
156C ALA* 4.3 8.5 - - + -
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Residues in contact with ILE 139 (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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53C LEU* 4.4 27.4 - - + -
54C VAL 3.3 17.0 - - - +
55C LEU* 4.0 23.8 - - + -
73C GLY 5.4 1.1 - - - +
138C ARG* 1.3 77.6 - - - +
140C GLU* 1.3 70.1 + - - +
141C SER* 4.2 3.8 - - - +
153C ILE* 3.8 1.0 - - + +
154C LYS* 3.3 4.2 - - - +
155C ILE* 2.7 63.7 + - + +
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Residues in contact with GLU 140 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C CYS* 5.2 0.2 - - - +
52C ASP 3.4 2.3 - - - +
53C LEU* 3.4 4.0 - - - -
54C VAL* 3.0 52.8 + - + +
139C ILE* 1.3 76.3 - - - +
141C SER* 1.3 63.7 + - - +
142C VAL* 4.0 18.1 - - + +
152C CYS* 4.1 15.8 - - - -
153C ILE 3.3 9.4 - - - +
154C LYS* 3.7 28.2 - - + +
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Residues in contact with SER 141 (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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51C VAL* 4.0 9.9 - - - +
52C ASP 3.3 3.8 - - - -
53C LEU* 3.2 23.7 - - - +
139C ILE* 4.2 5.5 - - - +
140C GLU* 1.3 73.4 - - - +
142C VAL* 1.3 64.3 + - - +
143C LEU* 4.1 1.2 + - - +
151C GLY 4.1 0.3 - - - +
152C CYS* 3.2 3.6 - - - -
153C ILE* 2.8 54.7 + - - +
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Residues in contact with VAL 142 (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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50C LYS 3.4 1.6 - - - +
51C VAL* 3.4 5.0 - - - +
52C ASP* 2.8 55.9 + - + +
140C GLU* 4.0 18.8 - - + +
141C SER* 1.3 78.2 + - - +
143C LEU* 1.3 65.8 + - - +
144C SER* 4.9 2.7 - - - -
149C ARG* 3.3 46.9 - - - +
151C GLY 3.5 2.7 - - - -
152C CYS* 3.6 21.8 - - - -
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Residues in contact with LEU 143 (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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15C ALA* 4.7 9.0 - - + -
45C LEU* 4.1 33.9 - - + -
49C LEU* 3.6 32.5 - - + -
50C LYS 3.3 12.8 - - - +
51C VAL* 3.8 18.4 - - + -
80C PHE* 5.7 0.9 - - + -
141C SER* 4.1 1.3 + - - +
142C VAL* 1.3 73.9 - - - +
144C SER* 1.3 63.6 + - - +
149C ARG* 3.8 3.3 - - - -
150C LEU* 2.7 29.3 + - + -
151C GLY* 2.8 20.8 + - - +
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Residues in contact with SER 144 (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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49C LEU* 3.6 5.0 - - - +
50C LYS* 2.8 57.0 + - - +
52C ASP* 4.4 4.2 + - - -
142C VAL* 4.9 6.7 - - - -
143C LEU* 1.3 77.8 - - - +
145C SER* 1.3 62.1 + - - +
147C GLY* 4.8 7.2 + - - -
148C LYS 3.2 22.4 - - - -
149C ARG* 4.2 7.0 - - - -
150C LEU* 3.8 6.1 - - - +
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Residues in contact with SER 145 (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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46C SER 3.4 12.5 + - - -
47C SER 4.5 0.5 + - - -
48C PRO* 2.6 28.9 + - - +
49C LEU* 4.5 0.2 - - - -
50C LYS* 5.7 0.7 - - - -
144C SER* 1.3 74.8 - - - +
146C SER* 1.3 63.9 + - - +
147C GLY 3.1 0.9 - - - -
148C LYS* 2.7 38.8 + - - +
150C LEU* 3.7 21.5 - - - +
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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