Contacts of the helix formed by residues 94 - 105 (chain K) in PDB entry 3GHG
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 ARG 94 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90K GLU* 2.9 38.6 + - - +
91K ARG* 3.7 21.8 - - - +
92K PRO 3.5 0.2 - - - -
93K ILE* 1.3 79.1 - - - +
95K ASN* 1.3 70.8 + - - +
96K SER 3.1 1.5 - - - +
97K VAL* 3.0 23.3 + - + +
98K ASP* 3.2 31.2 + - - +
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Residues in contact with ASN 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K ARG* 2.8 21.3 + - + +
92K PRO* 5.1 3.0 + - + +
94K ARG* 1.3 83.7 - - - +
96K SER* 1.3 68.0 + - - +
97K VAL 3.4 0.3 + - - -
98K ASP* 4.6 3.8 - - - +
99K GLU* 3.5 34.5 + - - +
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Residues in contact with SER 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66J ILE* 4.7 20.1 - - - +
70J LYS* 5.1 9.5 + - - +
92K PRO 3.4 22.8 + - - -
93K ILE* 4.3 7.6 - - - -
94K ARG 3.1 1.4 - - - +
95K ASN* 1.3 86.9 + - - +
97K VAL* 1.3 61.0 + - - +
99K GLU* 4.3 4.6 - - - +
100K LEU* 3.5 25.8 + - - +
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Residues in contact with VAL 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66J ILE* 5.5 6.5 - - + -
93K ILE* 3.1 30.3 - - + +
94K ARG* 3.0 12.5 + - + +
96K SER* 1.3 75.4 - - - +
98K ASP* 1.3 65.0 + - - +
99K GLU 3.1 1.8 - - - -
100K LEU* 2.8 25.2 + - - +
101K ASN* 3.1 24.0 + - - +
36L VAL* 5.7 7.6 - - + -
39L ASP* 5.6 8.3 - - + +
40L LEU* 5.0 19.3 - - + -
43L LEU* 5.8 3.1 - - + -
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Residues in contact with ASP 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94K ARG* 3.2 27.2 + - - +
95K ASN* 4.7 3.1 - - - +
97K VAL* 1.3 83.2 - - - +
99K GLU* 1.3 59.7 + - - +
101K ASN* 3.5 16.2 + - - +
102K ASN* 2.8 37.3 + - - +
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Residues in contact with GLU 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K ASN* 3.5 30.8 + - - +
96K SER* 4.3 5.1 - - - +
97K VAL 3.1 0.4 - - - -
98K ASP* 1.3 79.9 - - - +
100K LEU* 1.3 56.8 + - + +
102K ASN* 3.4 11.5 + - - +
103K ASN* 2.9 50.0 + - - +
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Residues in contact with LEU 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66J ILE* 3.5 26.2 - - + -
69J LEU* 2.8 39.9 - - + -
70J LYS* 4.4 13.2 - - + -
73J LEU* 4.8 16.4 - - + -
74J PHE* 6.2 0.7 - - + -
96K SER 3.5 10.5 + - - +
97K VAL* 2.8 11.4 + - - +
99K GLU* 1.3 77.9 - - + +
101K ASN* 1.3 59.6 + - - +
103K ASN* 3.1 14.2 + - + +
104K VAL* 2.8 39.0 + - + +
43L LEU* 3.6 17.5 - - + -
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Residues in contact with ASN 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K VAL* 3.1 23.4 + - - +
98K ASP* 3.7 18.8 + - - +
99K GLU 3.4 0.2 - - - -
100K LEU* 1.3 73.8 - - - +
102K ASN* 1.3 60.9 + - - +
105K GLU* 3.0 37.7 + - + +
106K ALA* 3.5 4.6 + - - +
39L ASP* 5.2 6.9 + - - +
43L LEU* 2.8 40.2 - - - +
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Residues in contact with ASN 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K ASP* 2.8 31.1 + - - +
99K GLU* 3.5 13.6 - - - +
101K ASN* 1.3 77.6 - - - +
103K ASN* 1.3 62.5 + - - +
106K ALA* 2.8 35.8 + - + +
107K VAL* 3.0 18.0 + - + +
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Residues in contact with ASN 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J LEU* 4.4 6.7 - - + +
77J GLN* 3.7 27.4 + - - +
99K GLU* 2.9 37.8 + - - +
100K LEU* 3.1 17.9 + - + +
102K ASN* 1.3 85.6 - - - +
104K VAL* 1.3 61.4 + - + +
107K VAL* 4.5 8.7 - - - +
108K SER* 3.3 19.3 + - - -
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Residues in contact with VAL 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J LEU* 5.7 1.8 - - + -
73J LEU* 4.3 15.7 - - + -
100K LEU* 2.8 25.2 + - + +
103K ASN* 1.3 79.3 - - + +
105K GLU* 1.3 80.8 + - - +
108K SER* 3.4 25.7 + - - +
43L LEU* 4.5 14.6 - - + +
46L ILE 4.2 0.7 - - - +
47L LEU* 3.5 50.5 - - + -
50L VAL* 4.4 8.1 - - + +
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Residues in contact with GLU 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101K ASN* 3.0 16.5 + - + +
104K VAL* 1.3 98.6 - - - +
106K ALA* 1.3 59.9 + - - +
107K VAL 3.5 1.3 - - - -
109K GLN* 3.2 34.4 - - - +
43L LEU* 3.3 23.2 - - - +
46L ILE* 3.2 53.4 - - + +
47L LEU 4.1 0.2 + - - -
50L VAL* 5.8 0.9 - - + -
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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