Contacts of the strand formed by residues 136 - 143 (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 LYS 136 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130F TRP* 3.5 9.9 - - - -
131F ASP* 2.7 40.6 + - - +
134F GLY* 3.2 22.9 - - - +
135F ASN* 1.3 74.5 - - - +
137F LEU* 1.3 67.6 - - - +
138F LEU* 3.8 16.9 + - + -
2H ALA* 2.7 41.5 + - - +
3H GLU* 4.1 5.9 - - - +
4H TYR* 4.1 29.9 - - + +
41H ASN* 5.0 0.8 + - - -
44H VAL* 4.6 17.9 - - + +
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Residues in contact with LEU 137 (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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95F LEU* 5.0 5.6 - - + -
98F ALA* 4.7 9.2 - - + -
99F ILE* 3.9 37.5 - - + +
102F ALA* 4.0 22.9 - - + +
103F PHE* 3.9 17.9 - - + -
128F LEU* 4.1 17.3 - - + -
129F GLY 3.5 8.3 - - - +
130F TRP* 3.7 20.9 - - + -
136F LYS* 1.3 74.4 - - - +
138F LEU* 1.3 69.9 + - - +
156F LEU* 3.6 29.6 - - + -
194F TYR* 4.3 9.0 - - + -
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Residues in contact with LEU 138 (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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103F PHE* 4.2 6.0 - - + -
127F ALA 3.8 0.2 - - - +
128F LEU* 3.5 3.2 - - - +
129F GLY 2.7 39.3 + - - +
131F ASP* 3.8 27.6 - - + -
136F LYS* 4.2 17.7 - - + +
137F LEU* 1.3 83.1 - - - +
139F ILE* 1.3 66.2 + - - +
140F PHE* 4.0 22.1 - - + -
4H TYR* 3.8 15.7 - - - +
44H VAL* 4.8 10.3 - - + -
47H LEU* 6.4 1.1 - - + -
66H LEU* 4.8 18.6 - - + -
70H LEU* 3.8 14.8 - - + -
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Residues in contact with ILE 139 (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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103F PHE* 3.5 34.1 - - + -
109F PHE* 3.8 26.2 - - + +
112F GLN* 3.5 30.2 + - + +
113F PHE* 3.9 23.3 - - + +
116F ALA* 4.1 15.9 - - + -
127F ALA 3.3 8.7 - - - +
128F LEU* 4.3 6.3 - - + -
138F LEU* 1.3 76.4 - - - +
140F PHE* 1.3 69.8 + - - +
63H GLU* 2.9 28.8 - - - +
66H LEU* 3.7 11.8 - - - +
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Residues in contact with PHE 140 (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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116F ALA* 4.8 0.4 - - - +
126F ALA* 3.8 3.8 - - - +
127F ALA* 2.8 41.2 + - + +
129F GLY 4.6 4.7 - - - -
138F LEU* 4.0 34.8 - - + -
139F ILE* 1.3 83.8 - - - +
141F GLN* 1.3 62.5 + - - +
142F VAL* 3.8 7.2 + - + -
148F ASN 4.3 11.9 - - - +
149F PHE* 4.1 19.1 - - + -
150F PRO* 3.5 24.9 - - + -
153F ILE* 3.6 44.2 - - + -
63H GLU* 3.7 4.3 - - - -
66H LEU* 4.2 22.7 - - + -
67H ALA* 4.7 8.5 - - + -
70H LEU* 4.4 2.7 - - + -
151H LEU* 5.7 2.2 - - + -
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Residues in contact with GLN 141 (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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116F ALA* 3.0 29.5 + - + +
119F THR* 2.7 40.4 + - - -
120F VAL* 3.7 16.5 - - + +
125F TRP 3.7 2.5 - - - +
126F ALA* 5.0 0.7 - - - +
140F PHE* 1.3 72.5 - - - +
142F VAL* 1.3 62.1 + - - +
143F TYR* 3.5 24.6 + - + -
148F ASN* 3.0 31.7 + - - +
59H ILE* 5.1 0.6 - - - +
60H LEU* 4.0 23.8 - - - +
63H GLU* 4.0 28.6 + - + +
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Residues in contact with VAL 142 (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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75F ASN* 5.1 1.1 - - - +
120F VAL* 4.5 2.6 - - - +
124F GLY* 3.0 5.0 - - - -
125F TRP* 3.0 48.0 + - + +
127F ALA* 4.4 20.9 - - + -
140F PHE* 4.7 6.1 - - + +
141F GLN* 1.3 73.2 - - - +
143F TYR* 1.3 74.9 + - - +
144F ASP 4.2 2.5 - - - +
145F HIS* 3.8 25.6 - - - +
147F THR 3.3 11.9 - - - +
148F ASN* 4.4 0.2 - - - -
149F PHE* 3.6 23.3 - - + -
151H LEU* 4.6 9.2 - - + -
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Residues in contact with TYR 143 (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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64E LYS* 4.7 17.0 + - - -
120F VAL* 4.5 12.8 - - + -
121F GLN 5.6 2.2 - - - -
123F CYS 3.8 5.4 - - - +
141F GLN* 3.5 34.2 + - - -
142F VAL* 1.3 77.7 - - - +
144F ASP* 1.3 76.4 + - - +
145F HIS 2.9 5.0 + - - -
147F THR* 2.8 47.3 + - + -
148F ASN* 3.4 26.6 + - + -
60H LEU* 4.4 13.2 + - + +
64H LYS* 3.7 29.3 - - + +
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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