Contacts of the strand formed by residues 153 - 160 (chain F) 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 ILE 153 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129F GLY* 4.4 5.2 - - - -
130F TRP 3.3 19.1 - - - +
131F ASP* 3.4 25.8 - - + +
140F PHE* 3.6 32.8 - - + -
149F PHE* 5.5 0.2 - - + -
150F PRO* 3.8 41.0 + - + +
151F LEU 3.3 2.7 - - - +
152F GLY* 1.3 77.1 - - - +
154F VAL* 1.3 71.0 + - - +
155F PRO* 3.4 0.9 - - - +
151H LEU* 4.2 21.5 - - + -
152H GLY* 3.3 24.5 + - - +
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Residues in contact with VAL 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F GLY* 3.0 5.2 - - - -
130F TRP* 2.6 57.6 + - + +
132F THR* 4.1 13.2 - - + -
152F GLY 4.4 2.7 - - - +
153F ILE* 1.3 74.6 - - - +
155F PRO* 1.3 78.5 - - + +
156F LEU* 3.6 5.0 + - + +
193F ARG* 5.3 1.6 - - + +
197F ALA* 4.2 25.6 - - + -
152H GLY* 5.0 1.1 - - - -
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Residues in contact with PRO 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F VAL* 5.4 1.3 - - + -
78F ILE* 3.7 27.8 - - + +
127F ALA* 6.1 0.4 - - + -
128F LEU 3.9 5.8 - - - +
129F GLY* 4.3 1.3 - - - -
153F ILE* 3.4 11.6 - - + +
154F VAL* 1.3 93.5 - - + +
156F LEU* 1.3 65.6 - - - +
158F LEU* 4.6 9.0 - - + -
193F ARG* 4.0 14.6 + - - +
151H LEU* 4.3 34.1 - - + +
152H GLY* 4.0 12.3 - - - +
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Residues in contact with LEU 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F ILE* 4.6 3.2 - - - +
82F ASN* 3.4 10.3 + - - -
95F LEU* 5.5 0.9 - - + -
128F LEU* 2.9 34.2 + - + +
129F GLY 4.3 3.8 - - - -
130F TRP* 4.3 2.9 - - + -
137F LEU* 3.6 31.2 - - + -
154F VAL* 3.9 12.8 - - + +
155F PRO* 1.3 82.0 - - - +
157F LEU* 1.3 60.6 + - - +
190F VAL* 4.1 15.3 - - + +
193F ARG* 3.3 56.1 - - + +
194F TYR* 3.8 19.3 - - + +
197F ALA* 4.2 9.9 - - + -
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Residues in contact with LEU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F ASN* 3.3 26.5 - - + +
109F PHE* 4.4 10.8 - - + -
113F PHE* 4.2 16.7 - - + -
127F ALA* 3.2 1.6 - - - -
128F LEU* 2.8 40.8 + - + +
156F LEU* 1.3 80.0 - - - +
158F LEU* 1.3 67.0 + - - +
181F PHE* 3.9 23.3 - - + -
182F TRP* 4.4 13.5 - - + -
185F VAL* 4.1 9.0 - - + -
187F TRP* 4.2 27.6 - - + -
190F VAL* 4.0 19.3 - - + -
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Residues in contact with LEU 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F VAL* 6.2 0.2 - - + -
75F ASN* 3.9 42.4 - - + +
78F ILE* 4.3 21.5 - - + -
79F TRP* 3.5 18.7 - - + -
82F ASN* 2.9 12.5 + - - +
113F PHE* 4.5 3.1 - - - -
125F TRP* 3.6 25.4 - - + -
126F ALA 3.3 3.8 - - - +
127F ALA* 3.0 33.4 - - + -
128F LEU 4.5 0.7 - - - +
155F PRO* 4.6 8.3 - - + -
157F LEU* 1.3 84.7 - - - +
159F LEU* 1.3 62.3 - - - +
160F ASP 4.1 0.4 - - - -
181F PHE* 3.8 10.2 - - - -
151H LEU* 4.2 11.9 - - + -
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Residues in contact with LEU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F TRP* 3.8 2.9 - - + -
113F PHE* 3.8 26.7 - - + -
114F HIS* 6.1 1.6 - - - -
117F ALA* 4.1 15.7 - - + -
125F TRP* 3.3 4.2 - - - -
126F ALA* 2.9 29.5 + - + +
158F LEU* 1.3 75.3 - - - +
160F ASP* 1.3 68.2 + - - +
161F MET* 3.3 11.7 + - - +
177F PHE* 3.5 36.3 - - + -
178F ALA* 4.2 19.3 - - + +
181F PHE* 3.7 39.3 - - + -
182F TRP* 5.7 0.4 - - - +
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Residues in contact with ASP 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F HIS* 2.9 14.7 + - - -
76F HIS* 3.6 1.7 + - - -
79F TRP* 3.6 17.5 - - + -
125F TRP* 3.3 30.9 - - + -
159F LEU* 1.3 71.2 - - - +
161F MET* 1.3 58.9 + - - +
162F TRP* 2.8 41.1 + - - +
164F HIS* 3.4 0.3 + - - -
165F ALA* 3.5 17.0 - - + +
177F PHE* 3.4 23.9 - - - -
999F FE 2.0 30.3 - - - -
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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