Contacts of the helix formed by residues 70 - 77 (chain D) 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 ILE 70 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ARG* 3.7 51.4 - - - +
152A LEU* 4.1 23.6 - - + -
69D PRO* 1.3 71.2 - - - +
71D PHE* 1.3 58.6 + - - +
73D ALA* 3.1 6.4 + - + +
74D ARG* 2.8 38.1 + - - +
151D PRO 5.1 0.2 - - - +
152D LEU* 3.2 14.2 + - + +
154D LEU* 2.9 46.1 + - + +
156D THR* 4.0 20.2 - - + -
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Residues in contact with PHE 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ARG* 4.0 33.7 - - - +
148A ILE* 3.6 29.8 - - + -
303A UMP 4.9 1.4 + - - -
69D PRO* 3.5 20.0 - - + -
70D ILE* 1.3 77.0 - - - +
72D VAL* 1.3 82.7 + - + +
74D ARG* 3.7 10.5 + - - +
75D GLN* 3.4 25.4 + - - +
99D TYR* 3.8 24.2 - + - -
152D LEU* 3.0 40.0 + - + +
153D ASN* 4.1 3.4 - - - -
180D GLN* 3.6 24.0 - - - -
182D GLU* 4.0 10.5 - - + -
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Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ALA* 4.1 5.4 - - + -
69D PRO* 3.0 27.8 + - + +
71D PHE* 1.3 97.8 - - + +
73D ALA* 1.3 66.9 + - - +
75D GLN* 3.0 11.8 + - - +
76D TRP* 3.0 30.3 + - + +
182D GLU* 3.8 20.4 - - + -
183D ILE* 3.8 26.5 - - + +
186D TYR* 4.1 19.5 - - + -
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Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ARG* 6.0 1.3 - - - +
68D ALA* 4.7 1.7 - - + +
69D PRO 3.0 11.8 + - - +
70D ILE* 3.7 7.2 - - + +
72D VAL* 1.3 77.8 - - - +
74D ARG* 1.3 56.3 + - + +
76D TRP* 4.0 7.9 - - - -
77D PHE* 2.7 45.2 + - + -
86D GLU* 4.7 4.9 - - - +
156D THR* 3.9 23.3 - - + -
158D PHE* 4.0 18.6 - - + -
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Residues in contact with ARG 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 3.7 33.1 + - - +
73A ALA* 4.2 5.1 + - - +
74A ARG* 3.7 50.6 - - + +
77A PHE* 5.4 4.6 - - - +
86A GLU* 2.8 39.3 + - - -
156A THR* 4.6 2.0 - - - +
303A UMP 3.8 17.9 + - + -
70D ILE* 2.8 37.5 + - - +
71D PHE* 3.9 7.4 - - - +
72D VAL 3.2 0.2 - - - -
73D ALA* 1.3 70.9 - - - +
75D GLN* 1.3 65.4 + - + +
77D PHE* 3.7 9.0 + - - +
78D ARG* 3.3 20.4 + - - +
152D LEU* 4.4 7.3 - - - +
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Residues in contact with GLN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 3.8 9.7 - - - +
147A ARG* 3.6 2.6 - - - +
303A UMP 3.0 63.4 + - + +
71D PHE* 3.4 15.4 + - - +
72D VAL* 3.0 8.8 + - - +
74D ARG* 1.3 75.6 - - + +
76D TRP* 1.3 65.4 + - - +
78D ARG* 3.1 15.4 + - - +
79D HIS* 3.9 0.3 - - - -
174D ARG* 3.1 21.4 + - - +
180D GLN* 3.2 27.6 + - - +
183D ILE* 3.5 34.3 - - + +
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Residues in contact with TRP 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 4.4 0.4 - - + -
66D VAL* 3.7 26.7 - - + -
68D ALA* 5.1 0.4 - - + -
72D VAL* 3.0 26.6 + - + +
73D ALA* 3.5 11.2 - - - +
75D GLN* 1.3 77.1 - - - +
77D PHE* 1.3 58.4 + - + +
78D ARG 3.1 5.2 + - - -
79D HIS* 3.1 21.2 + - - -
84D TYR* 3.4 19.6 + + - -
158D PHE* 3.8 15.5 - + - -
160D TRP* 3.4 51.0 - + - -
170D PHE* 3.6 23.2 - + - -
183D ILE* 3.8 12.9 - - + +
186D TYR* 3.4 42.6 - + + -
190D ILE* 4.1 15.5 - - + -
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Residues in contact with PHE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 6.5 0.4 - - + -
77A PHE* 4.6 15.7 - - + +
78A ARG* 3.6 34.1 - - - -
80A ARG* 5.8 2.1 - - - +
73D ALA* 2.7 37.3 + - + +
74D ARG* 4.3 5.8 - - - +
75D GLN 3.3 0.6 - - - -
76D TRP* 1.3 70.7 - - + +
78D ARG* 1.3 61.3 + - - +
79D HIS 3.1 11.6 + - - +
80D ARG* 5.0 4.3 - - - +
84D TYR* 3.6 53.0 - + + -
86D GLU* 3.7 23.6 - - + -
158D PHE* 3.7 44.2 - + + -
318D UMP 4.4 2.2 - - - -
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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
------------------------------------------------------------
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