Contacts of the strand formed by residues 136 - 143 (chain A) in PDB entry 1GN3
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A TRP* 3.1 11.9 - - - -
131A ASP* 2.5 34.0 + - + +
134A GLY* 3.0 22.4 - - - +
135A ASN* 1.3 81.1 - - - +
137A LEU* 1.3 60.3 - - - +
138A LEU* 3.8 28.9 - - + -
2B ALA* 3.1 29.2 + - - +
3B GLU* 5.0 1.0 - - - +
4B TYR* 3.5 36.7 - - - +
41B ASN* 5.2 1.2 + - - -
44B VAL* 4.0 22.2 - - + +
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Residues in contact with LEU 137 (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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95A LEU* 4.8 3.6 - - + -
98A ALA* 3.9 34.5 - - + -
99A ILE* 4.3 11.4 - - + +
102A ALA* 3.5 24.6 - - + +
103A PHE* 3.3 25.7 - - + -
128A LEU* 4.0 10.1 - - + -
129A GLY 3.6 11.2 - - - +
130A TRP* 4.0 19.6 - - + -
136A LYS* 1.3 71.5 - - - +
138A LEU* 1.3 70.2 + - - +
156A LEU* 3.5 29.6 - - + -
194A TYR* 4.4 9.2 - - + -
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Residues in contact with LEU 138 (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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103A PHE* 4.1 2.5 - - + -
128A LEU* 3.1 7.8 - - - +
129A GLY 2.6 42.2 + - - -
131A ASP* 3.8 28.7 - - + +
136A LYS* 3.8 25.4 - - + -
137A LEU* 1.3 80.4 - - - +
139A ILE* 1.3 67.6 + - - +
140A PHE* 4.0 26.7 - - + -
4B TYR* 4.1 10.1 - - - +
44B VAL* 4.4 7.9 - - + -
47B LEU* 6.0 3.4 - - + -
66B LEU* 4.3 24.7 - - + -
70B LEU* 4.2 7.9 - - + -
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Residues in contact with ILE 139 (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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103A PHE* 3.4 29.2 - - + -
109A PHE* 3.5 31.0 - - + +
112A GLN* 3.8 26.2 + - + +
113A PHE* 4.2 14.4 - - + -
116A ALA* 3.9 21.3 - - + -
127A ALA 3.1 8.5 - - - +
128A LEU* 4.2 7.2 - - + -
138A LEU* 1.3 82.4 - - - +
140A PHE* 1.3 62.0 + - - +
47B LEU* 4.9 0.9 - - - +
63B GLU* 2.6 37.8 - - - +
66B LEU* 3.9 12.0 - - - +
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Residues in contact with PHE 140 (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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116A ALA* 4.9 0.6 - - - +
126A ALA* 3.8 1.4 - - - -
127A ALA* 2.7 40.6 + - + +
129A GLY* 4.3 6.5 - - - -
138A LEU* 4.0 35.2 - - + -
139A ILE* 1.3 81.9 - - - +
141A GLN* 1.3 61.2 + - - +
142A VAL* 3.8 8.5 + - + -
148A ASN 4.4 5.6 - - - +
149A PHE* 3.9 27.6 - - + -
150A PRO* 3.4 18.8 - - + -
153A ILE* 3.7 42.0 - - + -
63B GLU* 3.3 8.1 - - - -
66B LEU* 4.2 18.6 - - + -
67B ALA* 4.5 7.4 - - + -
70B LEU* 4.2 5.8 - - + -
151B LEU* 5.7 2.5 - - + -
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Residues in contact with GLN 141 (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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116A ALA* 2.9 23.6 + - - +
119A THR* 2.7 43.2 + - - -
120A VAL* 3.9 15.9 - - + -
125A TRP 3.8 3.4 - - - +
126A ALA* 5.0 1.8 - - - +
140A PHE* 1.3 72.4 - - - +
142A VAL* 1.3 63.5 + - - +
143A TYR* 3.5 25.5 + - + -
148A ASN* 3.1 27.3 + - - +
59B ILE* 5.1 0.2 - - - +
60B LEU* 3.7 29.7 - - - +
63B GLU* 3.7 24.1 + - + +
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Residues in contact with VAL 142 (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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75A ASN* 5.4 2.0 - - - +
120A VAL* 4.4 1.9 - - - +
124A GLY* 2.9 5.9 - - - -
125A TRP* 2.7 56.8 + - + +
127A ALA* 4.1 24.9 - - + -
140A PHE* 4.5 6.3 - - + +
141A GLN* 1.3 73.6 - - - +
143A TYR* 1.3 72.5 + - - +
145A GLN* 4.3 11.7 - - - +
147A THR 3.5 5.4 - - - +
148A ASN* 4.5 0.7 - - - -
149A PHE* 3.2 42.8 - - + -
158A LEU* 5.6 0.2 - - + -
151B LEU* 4.8 7.9 - - + -
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Residues in contact with TYR 143 (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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120A VAL* 4.4 13.0 - - + -
121A GLN 5.5 2.9 - - - -
123A SER 4.1 5.4 - - - +
141A GLN* 3.6 32.9 + - - -
142A VAL* 1.3 75.6 - - - +
144A ASP* 1.3 73.6 + - + +
145A GLN 3.0 4.2 + - - -
146A GLN 3.5 0.3 + - - -
147A THR* 2.8 43.2 + - + +
148A ASN* 3.7 30.2 + - + -
60B LEU* 4.0 14.3 - - + +
64B LYS* 3.7 39.8 - - - +
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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