Contacts of the strand formed by residues 61 - 69 (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 VAL 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C VAL* 3.3 5.8 - - - +
17C MET* 2.9 62.5 + - + -
58C GLU 3.9 12.8 - - - +
60C ILE* 1.3 85.2 - - - +
62C PHE* 1.3 66.6 + - - +
161C THR* 4.0 24.9 - - + -
162C VAL 3.6 12.8 - - - +
163C ASN* 4.2 5.2 - - + -
17D MET* 3.7 12.7 - - + +
61D VAL* 4.2 13.5 - - + -
161D THR* 4.6 2.2 - - + -
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Residues in contact with PHE 62 (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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13C LEU* 4.0 18.8 - - + -
15C ASP 3.6 3.4 - - - +
16C VAL* 4.0 10.3 - - + -
60C ILE* 3.8 17.9 - - + -
61C VAL* 1.3 78.6 - - - +
63C THR* 1.3 62.0 + - - +
64C PHE* 3.4 29.2 - + + -
160C TRP 3.7 1.1 - - - +
161C THR* 3.2 6.1 - - - +
162C VAL* 2.9 36.1 + - + +
164C ALA* 4.6 5.8 - - + -
167C LEU* 3.8 14.4 - - + -
193C ILE* 4.4 2.0 - - + -
194C PHE* 3.7 43.7 - + - -
197C LYS* 3.8 26.0 - - + -
198C CYS* 3.9 14.4 - - - -
17D MET* 4.6 0.4 - - - -
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Residues in contact with THR 63 (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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13C LEU* 3.5 4.0 - - - +
14C VAL* 2.7 39.8 + - + -
15C ASP* 2.9 25.8 + - - +
62C PHE* 1.3 69.7 - - - +
64C PHE* 1.3 60.8 + - - +
159C PHE* 3.8 28.5 - - + -
160C TRP 3.2 6.5 - - - +
161C THR* 2.7 24.5 + - - +
17D MET* 3.4 21.1 - - - +
59D HIS* 4.3 8.6 + - + +
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Residues in contact with PHE 64 (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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11C VAL* 3.7 17.9 - - + -
12C GLU 3.2 11.0 - - - +
13C LEU* 4.2 6.5 - - + -
14C VAL* 4.0 3.4 - - - -
62C PHE* 3.4 36.8 - + + -
63C THR* 1.3 78.4 - - - +
65C HIS* 1.3 58.4 + - - +
66C VAL* 4.0 17.9 - - + -
159C PHE* 3.4 5.4 - - - -
160C TRP* 2.8 60.7 + + + +
162C VAL* 3.9 13.0 - - + -
167C LEU* 4.4 10.8 - - + -
190C ILE* 3.7 21.5 - - + -
193C ILE* 3.8 31.6 - - + -
194C PHE 5.4 0.2 - - - -
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Residues in contact with HIS 65 (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* 3.7 21.9 - + - -
11C VAL* 3.7 0.9 - - - -
12C GLU* 2.8 58.8 + - - +
14C VAL* 3.6 19.8 - - + +
64C PHE* 1.3 72.1 - - - +
66C VAL* 1.3 67.5 + - - +
157C ARG* 3.1 39.6 + - - -
158C PHE 3.5 11.7 - - - -
159C PHE* 3.6 19.8 - + + -
29D VAL* 3.7 10.3 + - + +
30D SER* 5.0 0.4 - - - -
31D PHE 4.3 11.3 + - - -
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Residues in contact with VAL 66 (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* 3.4 9.6 - - - +
11C VAL* 4.4 11.4 - - + -
64C PHE* 4.0 18.4 - - + -
65C HIS* 1.3 79.6 - - - +
67C LYS* 1.3 69.7 + - - +
68C ALA* 4.0 4.7 - - + -
76C TRP* 3.8 38.8 - - + -
157C ARG* 3.2 3.5 - - - +
158C PHE* 2.9 68.4 + - + +
160C TRP* 5.0 0.9 - - + -
186C TYR* 4.2 2.9 - - + -
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Residues in contact with LYS 67 (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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8C LYS* 2.9 28.3 + - - +
9C GLY* 3.3 1.9 - - - -
10C PHE* 2.9 52.8 + - + +
66C VAL* 1.3 72.3 - - - +
68C ALA* 1.3 54.4 + - - +
97C GLU* 2.9 35.1 + - - -
155C TYR* 4.0 21.3 - - + -
156C THR 3.2 8.3 - - - +
157C ARG* 3.4 25.8 - - + +
186C TYR* 2.5 26.2 + - - -
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Residues in contact with ALA 68 (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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66C VAL* 4.0 10.9 - - + -
67C LYS* 1.3 77.1 - - - +
69C PRO* 1.3 70.8 - - + +
72C VAL* 4.0 15.7 - - + -
73C ALA 4.7 4.0 - - - +
76C TRP* 5.1 0.4 - - + -
155C TYR* 3.5 7.2 - - - -
156C THR* 2.6 45.0 + - + +
158C PHE* 4.7 7.4 - - + -
186C TYR* 3.2 17.3 - - + +
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Residues in contact with PRO 69 (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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6C LEU* 4.0 14.8 - - + -
68C ALA* 1.3 89.1 - - + +
70C ILE* 1.3 58.3 + - - +
71C PHE* 3.7 31.4 - - + -
72C VAL* 2.8 38.4 + - + -
73C ALA 2.9 11.3 + - - -
99C TYR* 4.0 10.5 - - + -
153C ASN* 3.6 20.4 - - - +
154C LEU 3.1 6.7 - - - +
155C TYR* 3.7 10.0 - - + -
156C THR* 4.4 0.4 - - - -
186C TYR* 3.8 9.0 - - - +
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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