Contacts of the strand formed by residues 155 - 163 (chain C) in PDB entry 3G4C
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 TYR 155 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.4 17.2 - - - +
7C ASP* 2.6 25.5 + - - -
8C LYS* 3.1 23.3 + - + -
9C GLY* 3.6 20.9 - - - -
67C LYS* 4.0 24.2 - - + -
68C ALA* 3.5 21.3 - - - -
69C PRO* 3.8 13.7 - - + -
70C ILE* 5.6 0.2 - - - +
87C LEU* 5.3 2.8 - - - +
94C LEU* 5.0 6.6 - - - +
95C SER 5.7 0.2 - - - +
97C GLU* 2.9 20.3 + - + +
98C PHE 3.5 23.8 - - - -
99C TYR* 3.3 29.7 - - + +
153C ASN 3.4 1.1 + - - -
154C LEU* 1.3 85.9 - - - +
156C THR* 1.3 58.3 + - - +
186C TYR* 3.9 2.7 - - - -
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Residues in contact with THR 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ARG* 4.5 0.4 + - - -
67C LYS* 3.2 5.2 - - - +
68C ALA 2.6 52.1 + - - +
70C ILE* 4.2 16.2 - - + +
73C ALA* 3.6 25.6 - - + -
86C GLU* 2.5 38.4 + - - +
87C LEU* 4.6 11.6 + - - +
94C LEU* 6.4 0.7 - - - -
154C LEU 3.7 0.2 + - - -
155C TYR* 1.3 73.9 - - - +
157C ARG* 1.3 66.2 + - - +
158C PHE* 4.6 7.8 - - + -
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Residues in contact with ARG 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 4.0 12.3 - - - -
65C HIS* 3.1 25.2 + - - +
66C VAL 3.2 4.3 - - - +
67C LYS* 3.4 38.7 - - + +
86C GLU* 3.4 2.4 - - - +
87C LEU* 2.9 55.5 + - + +
156C THR* 1.3 75.8 + - - +
158C PHE* 1.3 64.7 + - - +
28D ARG 5.5 1.6 + - - -
29D VAL* 2.7 35.7 + - + +
30D SER* 4.9 1.2 + - - +
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Residues in contact with PHE 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C PHE 3.9 0.3 - - - +
65C HIS* 3.5 1.8 - - - -
66C VAL* 2.9 68.5 + - + +
68C ALA* 4.7 6.3 - - + -
73C ALA* 4.4 13.0 - - + -
76C TRP* 3.9 22.7 - + - -
77C PHE* 3.6 34.1 - + + -
84C TYR* 4.1 7.0 - + - -
85C ASN 3.2 15.5 - - - +
86C GLU* 3.6 12.3 - - + -
156C THR* 4.6 10.8 - - + -
157C ARG* 1.3 79.3 - - - +
159C PHE* 1.3 71.5 + - - +
160C TRP* 3.9 20.9 - + + -
29D VAL* 3.7 8.5 - - - -
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Residues in contact with PHE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL* 3.6 35.0 - - + -
63C THR* 3.8 16.6 - - + -
64C PHE 3.4 2.7 - - - -
65C HIS* 3.6 35.9 - + + -
83C SER 3.7 0.2 - - - +
84C TYR* 3.2 7.6 - - - -
85C ASN* 2.8 36.5 + - + +
158C PHE* 1.3 76.5 - - - +
160C TRP* 1.3 58.1 + - - +
22D SER 5.0 2.2 - - - -
25D ARG* 4.1 8.7 - - + -
26D ALA* 3.7 34.1 - - + +
29D VAL* 3.9 9.8 - - + +
30D SER 3.9 32.1 - - - -
31D PHE 4.2 2.0 - - - -
59D HIS* 3.9 14.0 - + + -
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Residues in contact with TRP 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PHE 3.7 1.0 - - - +
63C THR* 3.2 3.1 - - - -
64C PHE* 2.8 66.2 + + + +
66C VAL* 5.0 0.2 - - + -
76C TRP* 3.3 43.7 - + - -
79C HIS* 5.2 3.1 - - + -
82C ALA* 3.2 20.5 - - + +
83C SER 3.3 10.8 - - - -
84C TYR* 3.1 34.1 + + - -
158C PHE* 3.9 12.9 + - + -
159C PHE* 1.3 73.2 - - - +
161C THR* 1.3 61.6 + - - +
162C VAL* 3.8 33.0 - - + -
166C SER* 5.4 0.9 - - - -
167C LEU* 3.9 11.0 - - + -
170C PHE* 3.9 27.6 - + + -
190C ILE* 4.0 14.1 - - + -
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Residues in contact with THR 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL* 4.0 22.0 - - + -
62C PHE 3.2 4.5 - - - +
63C THR* 2.7 22.5 + - - +
82C ALA* 3.3 3.9 - - - +
83C SER* 2.8 39.8 + - - +
160C TRP* 1.3 68.9 - - - +
162C VAL* 1.4 60.5 + - - +
17D MET* 4.2 7.6 - - + -
58D GLU 3.8 18.6 - - - +
59D HIS* 2.7 32.1 + - - +
61D VAL* 4.3 3.4 - - + -
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Residues in contact with VAL 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL* 4.4 3.4 - - - -
62C PHE* 2.9 30.1 + - + +
64C PHE* 3.9 17.0 - - + -
81C ILE 4.2 2.0 - - - +
82C ALA* 4.3 4.5 - - + +
160C TRP* 3.8 47.1 - - + +
161C THR* 1.4 75.0 - - - +
163C ASN* 1.4 74.0 + - - +
166C SER* 3.6 16.2 - - - +
167C LEU* 3.4 26.7 - - + +
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Residues in contact with ASN 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A FAD 2.7 32.7 + - - -
58C GLU* 3.4 26.2 + - - +
60C ILE 3.1 13.9 - - - +
61C VAL* 4.0 8.3 - - + +
62C PHE* 5.2 0.4 - - - -
81C ILE* 4.8 2.8 + - - +
162C VAL* 1.4 77.1 - - - +
164C ALA* 1.3 59.0 - - - +
165C ARG* 2.6 33.0 + - - +
166C SER* 2.7 16.9 + - - -
167C LEU* 2.8 26.3 + - - +
83D SER* 4.7 1.2 + - - -
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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