Contacts of the strand formed by residues 136 - 143 (chain D) in PDB entry 1GN2
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 136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ALA* 2.8 41.0 + - - +
3B GLU* 3.9 8.3 - - - +
4B TYR* 4.0 29.0 - - + +
41B ASN* 4.7 1.0 + - - -
44B VAL* 4.4 18.5 - - + +
102D ALA* 6.4 0.2 - - + -
130D TRP* 3.5 9.9 - - - -
131D ASP* 2.7 40.6 + - - +
134D GLY* 3.2 20.0 - - - +
135D ASN* 1.3 75.2 - - - +
137D LEU* 1.3 66.5 - - - +
138D LEU* 3.8 16.3 + - + -
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D LEU* 5.0 5.4 - - + -
98D ALA* 4.7 8.3 - - + -
99D ILE* 3.9 37.2 - - + +
102D ALA* 4.0 23.4 - - + +
103D PHE* 3.9 16.8 - - + -
128D LEU* 4.1 17.5 - - + -
129D GLY 3.5 7.9 - - - +
130D TRP* 3.7 20.6 - - + -
136D LYS* 1.3 74.4 - - - +
138D LEU* 1.3 69.8 + - - +
156D LEU* 3.6 29.4 - - + -
194D TYR* 4.3 9.4 - - + -
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B TYR* 3.7 22.2 - - - +
44B VAL* 4.6 21.1 - - + -
47B LEU* 6.2 2.0 - - + -
66B LEU* 4.6 15.3 - - + -
70B LEU* 3.7 19.3 - - + -
103D PHE* 4.2 6.9 - - + -
127D ALA 3.8 0.2 - - - +
128D LEU* 3.5 2.5 - - - +
129D GLY 2.7 39.5 + - - +
131D ASP* 3.8 16.4 - - + -
136D LYS* 4.2 13.9 - - + +
137D LEU* 1.3 83.2 - - - +
139D ILE* 1.3 64.9 + - - +
140D PHE* 4.0 20.7 - - + -
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Residues in contact with ILE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLU* 2.7 35.8 - - - +
66B LEU* 3.6 12.4 - - - +
103D PHE* 3.5 35.0 - - + -
109D PHE* 3.8 25.4 - - + +
112D GLN* 3.5 30.7 + - + +
113D PHE* 3.9 22.9 - - + +
116D ALA* 4.1 15.3 - - + -
127D ALA 3.3 8.7 - - - +
128D LEU* 4.3 6.5 - - + -
138D LEU* 1.3 75.5 - - - +
140D PHE* 1.3 64.7 + - - +
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Residues in contact with PHE 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLU* 3.5 6.3 - - - -
66B LEU* 4.0 22.4 - - + -
67B ALA* 4.5 8.5 - - + -
70B LEU* 4.3 2.5 - - + -
151B LEU* 5.9 2.0 - - + -
116D ALA* 4.8 0.6 - - - +
126D ALA* 3.8 3.6 - - - -
127D ALA* 2.8 41.0 + - + +
128D LEU 5.4 0.2 - - - -
129D GLY* 4.6 4.5 - - - -
138D LEU* 4.0 34.5 - - + -
139D ILE* 1.3 81.8 - - - +
141D GLN* 1.3 62.0 + - - +
142D VAL* 3.8 7.6 + - + -
148D ASN 4.3 12.3 - - - +
149D PHE* 4.1 17.9 - - + -
150D PRO* 3.5 23.8 - - + -
153D ILE* 3.6 45.3 - - + -
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Residues in contact with GLN 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 4.9 0.2 - - - +
60B LEU* 3.7 30.1 - - - +
63B GLU* 3.8 26.4 + - + +
116D ALA* 3.0 29.3 + - + +
119D THR* 2.7 41.2 + - - -
120D VAL* 3.7 15.2 - - + +
125D TRP 3.7 3.1 - - - +
126D ALA* 5.0 0.2 - - - +
140D PHE* 1.3 72.7 - - - +
142D VAL* 1.3 60.4 + - - +
143D TYR* 3.5 22.9 + - + -
148D ASN* 3.0 30.5 + - - +
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LEU* 4.8 8.3 - - + -
75D ASN* 5.1 1.6 - - - +
120D VAL* 4.5 2.4 - - - +
124D GLY* 3.0 5.0 - - - -
125D TRP* 3.0 47.2 + - + +
127D ALA* 4.4 21.5 - - + -
140D PHE* 4.7 5.8 - - + +
141D GLN* 1.3 74.4 - - - +
143D TYR* 1.3 75.3 + - - +
144D ASP 4.2 2.5 - - - +
145D HIS* 3.8 26.0 - - - +
147D THR 3.3 12.1 - - - +
148D ASN* 4.4 0.2 - - - -
149D PHE* 3.6 24.2 - - + -
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Residues in contact with TYR 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 4.3 13.2 + - + +
64B LYS* 3.6 29.8 - - + +
64C LYS* 4.7 14.3 + - - -
120D VAL* 4.5 13.0 - - + -
121D GLN 5.6 1.8 - - - -
123D CYS 3.8 5.4 - - - +
141D GLN* 3.5 34.7 + - + -
142D VAL* 1.3 76.4 - - - +
144D ASP* 1.3 76.3 + - - +
145D HIS 2.9 4.9 + - - -
147D THR* 2.8 47.0 + - + -
148D ASN* 3.4 26.2 + - + -
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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