Contacts of the strand formed by residues 154 - 160 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B GLY* 3.3 0.5 - - - -
130B TRP* 2.9 38.9 + - + +
132B THR* 4.6 7.4 - - + -
152B ALA 4.1 8.1 - - - +
153B ILE* 1.3 79.0 - - - +
155B PRO* 1.3 77.2 - - + +
156B LEU* 3.6 6.4 - - + +
193B ARG* 4.9 3.8 - - + +
197B ALA* 3.9 32.8 - - + +
152D ALA* 4.8 4.9 - - + +
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Residues in contact with PRO 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B VAL* 5.3 0.2 - - + -
78B ILE* 3.4 30.9 - - + +
127B ALA* 5.8 0.9 - - + -
128B LEU 3.8 5.4 - - - +
129B GLY* 4.3 2.2 - - - -
153B ILE* 3.7 3.5 - - - +
154B VAL* 1.3 91.1 - - + +
156B LEU* 1.3 65.2 + - - +
158B LEU* 4.5 12.6 - - + -
193B ARG* 3.9 15.2 + - - +
151D LEU* 4.1 33.7 - - + -
152D ALA* 3.6 23.6 - - + +
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 5.0 2.2 - - - -
82B ASN* 3.3 10.5 + - - -
95B LEU* 5.0 3.1 - - + -
128B LEU* 2.7 32.4 + - + +
129B GLY* 4.4 2.7 - - - -
130B TRP* 4.6 3.4 - - + -
137B LEU* 3.3 33.7 - - + -
154B VAL* 3.6 18.8 - - + +
155B PRO* 1.3 82.4 - - - +
157B LEU* 1.3 58.6 + - - +
190B VAL* 3.8 15.5 - - + +
193B ARG* 3.2 51.3 - - + +
194B TYR* 4.1 22.7 - - + -
197B ALA* 4.4 4.7 - - + -
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ASN* 3.2 24.7 - - + +
109B PHE* 4.2 13.2 - - + -
113B PHE* 4.1 14.1 - - + -
126B ALA 4.0 0.2 - - - +
127B ALA* 3.6 0.9 - - - -
128B LEU* 3.0 40.8 + - + -
156B LEU* 1.3 78.9 - - - +
158B LEU* 1.3 67.7 + - - +
181B PHE* 3.9 19.7 - - + -
182B TRP* 4.2 17.0 - - + -
185B VAL* 4.0 9.4 - - + -
187B TRP* 4.0 29.6 - - + -
190B VAL* 3.8 15.3 - - + -
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ASN* 3.7 44.0 - - + +
78B ILE* 4.2 20.4 - - + -
79B TRP* 3.3 21.1 - - + +
82B ASN* 2.8 14.6 + - - +
113B PHE* 4.5 2.2 - - - -
125B TRP* 3.8 20.6 - - + -
126B ALA 3.4 3.4 - - - +
127B ALA* 3.1 33.4 - - + -
142B VAL* 5.6 0.4 - - + -
155B PRO* 4.5 9.6 - - + -
157B LEU* 1.3 78.8 - - - +
159B LEU* 1.3 60.7 + - - +
160B ASP 4.1 0.4 - - - -
181B PHE* 3.9 8.9 - - - -
151D LEU* 4.3 14.8 - - + -
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TRP* 3.9 6.1 - - + -
113B PHE* 3.7 25.3 - - + -
114B HIS* 6.2 0.4 - - - -
117B ALA* 3.5 27.8 - - + -
125B TRP* 3.1 10.5 - - - -
126B ALA 3.0 28.9 + - - +
158B LEU* 1.3 75.0 - - - +
160B ASP* 1.3 62.4 + - - +
161B MET* 3.4 11.1 + - - +
177B PHE* 3.8 26.7 - - + -
178B ALA* 4.2 15.0 - - + +
181B PHE* 3.8 36.3 - - + -
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Residues in contact with ASP 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B HIS* 2.8 15.4 + - - -
76B HIS* 3.3 1.9 + - - -
79B TRP* 3.7 17.4 - - + -
125B TRP* 3.3 30.5 - - + -
159B LEU* 1.3 70.1 - - - +
161B MET* 1.3 61.1 + - - +
162B TRP* 3.1 26.2 + - - +
164B HIS* 3.5 0.3 + - - -
165B ALA* 3.5 16.4 - - + +
177B PHE* 3.4 24.3 - - - -
999B FE 2.0 32.8 - - - -
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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