Contacts of the strand formed by residues 154 - 160 (chain A) in PDB entry 1GN6
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 VAL 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLY* 3.3 0.5 - - - -
130A TRP* 2.9 39.6 + - + +
132A THR* 4.6 7.2 - - + -
152A ALA 4.1 8.5 - - - +
153A ILE* 1.3 77.0 - - - +
155A PRO* 1.3 76.0 - - + +
156A LEU* 3.6 6.5 - - + +
193A ARG* 4.9 4.0 - - + +
196A ALA* 6.5 0.2 - - + -
197A ALA* 3.9 32.8 - - + +
152C ALA* 4.8 4.5 - - + +
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Residues in contact with PRO 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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74A VAL* 5.3 0.2 - - + -
78A ILE* 3.4 30.4 - - + +
127A ALA* 5.8 0.2 - - + -
128A LEU 3.8 5.6 - - - +
129A GLY* 4.3 2.2 - - - -
153A ILE* 3.7 3.8 - - - +
154A VAL* 1.3 90.2 - - + +
156A LEU* 1.3 65.0 + - - +
158A LEU* 4.5 13.2 - - + -
193A ARG* 3.9 15.2 + - - +
151C LEU* 4.2 33.9 - - + -
152C ALA* 3.7 23.1 - - + +
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Residues in contact with LEU 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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78A ILE* 5.0 2.2 - - - -
82A ASN* 3.3 10.7 + - - -
95A LEU* 5.0 3.6 - - + -
128A LEU* 2.7 30.6 + - + +
129A GLY* 4.4 2.5 - - - -
130A TRP* 4.6 3.1 - - + -
137A LEU* 3.3 34.1 - - + -
154A VAL* 3.6 18.6 - - + +
155A PRO* 1.3 82.9 - - - +
157A LEU* 1.3 58.6 + - - +
190A VAL* 3.8 14.8 - - + +
193A ARG* 3.2 50.8 - - + +
194A TYR* 4.0 22.7 - - + +
197A ALA* 4.4 4.9 - - + -
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Residues in contact with LEU 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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82A ASN* 3.2 26.9 - - + +
109A PHE* 4.3 13.0 - - + -
113A PHE* 4.1 14.3 - - + -
127A ALA* 3.6 0.7 - - - -
128A LEU* 3.0 41.4 + - + -
156A LEU* 1.3 78.0 - - - +
158A LEU* 1.3 67.8 + - - +
181A PHE* 3.9 19.7 - - + -
182A TRP* 4.2 16.4 - - + -
185A VAL* 4.0 9.0 - - + -
187A TRP* 4.0 30.3 - - + -
190A VAL* 3.8 14.6 - - + -
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Residues in contact with LEU 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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75A ASN* 3.7 44.4 - - + +
78A ILE* 4.2 20.6 - - + -
79A TRP* 3.3 20.4 - - + +
82A ASN* 2.8 15.1 + - - +
113A PHE* 4.5 2.7 - - - -
125A TRP* 3.8 21.8 - - + -
126A ALA 3.4 3.6 - - - +
127A ALA* 3.1 33.0 - - + -
128A LEU 4.8 0.2 - - - +
142A VAL* 5.6 0.4 - - + -
155A PRO* 4.5 9.2 - - + -
157A LEU* 1.3 79.4 - - - +
159A LEU* 1.3 61.5 + - - +
160A ASP 4.1 0.4 - - - -
181A PHE* 3.9 8.2 - - - -
151C LEU* 4.3 14.8 - - + -
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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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79A TRP* 3.9 5.6 - - + -
113A PHE* 3.7 26.7 - - + -
114A HIS* 6.2 0.7 - - - -
117A ALA* 3.5 27.6 - - + -
125A TRP* 3.1 10.9 - - - -
126A ALA 3.0 30.0 + - - +
158A LEU* 1.3 74.0 - - - +
160A ASP* 1.3 61.1 + - - +
161A MET* 3.4 11.4 + - - +
177A PHE* 3.8 26.5 - - + -
178A ALA* 4.2 14.4 - - + +
181A PHE* 3.8 35.2 - - + -
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Residues in contact with ASP 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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28A HIS* 2.8 14.9 + - - -
76A HIS* 3.3 2.3 + - - -
79A TRP* 3.7 18.3 - - + -
125A TRP* 3.3 30.9 - - + -
159A LEU* 1.3 70.2 - - - +
161A MET* 1.3 59.6 + - - +
162A TRP* 3.1 25.8 + - - +
164A HIS* 3.5 0.5 + - - -
165A ALA* 3.5 16.3 - - + +
177A PHE* 3.4 24.8 - - - -
999A FE 2.0 33.2 - - - -
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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