Contacts of the helix formed by residues 97 - 110 (chain C) in PDB entry 3GXM
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 SER 97 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B THR* 6.1 5.4 - - - -
20C ALA* 3.7 13.5 - - - +
95C ALA 4.2 0.8 + - - -
96C LEU* 1.3 71.4 - - - +
98C PRO* 1.4 77.9 - - - +
99C PRO* 3.7 7.0 - - - +
100C ALA* 2.9 14.0 + - - +
101C GLN 3.0 9.4 + - - -
409C ASP* 2.4 36.9 + - - -
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Residues in contact with PRO 98 (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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96C LEU 3.8 0.2 - - - -
97C SER* 1.4 83.4 - - - +
99C PRO* 1.4 67.0 - - + +
101C GLN* 3.1 26.6 + - - +
102C ASN* 3.1 32.9 + - - +
163C ARG* 5.7 0.4 - - - +
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Residues in contact with PRO 99 (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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20C ALA* 3.4 24.9 - - + +
97C SER* 3.2 16.2 - - - +
98C PRO* 1.4 97.3 - - + +
100C ALA* 1.3 60.4 + - - +
102C ASN* 3.4 10.3 + - + +
103C LEU* 3.2 26.7 + - - +
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Residues in contact with ALA 100 (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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19C ASN 3.9 16.8 - - - +
20C ALA* 3.8 17.8 - - - +
96C LEU* 3.9 16.1 - - + +
97C SER* 2.9 10.6 + - - +
99C PRO* 1.3 78.4 - - - +
101C GLN* 1.3 63.4 + - - +
103C LEU* 3.4 1.0 + - - +
104C LEU* 3.1 18.9 + - - +
409C ASP* 3.7 20.6 - - - +
411C PHE* 3.3 12.7 - - + -
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Residues in contact with GLN 101 (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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93C ILE* 3.4 26.8 - - + +
94C LEU* 3.7 26.8 + - - +
96C LEU* 2.9 27.7 + - - +
97C SER 3.0 14.6 + - - +
98C PRO* 3.2 26.8 - - - +
100C ALA* 1.3 74.1 - - - +
102C ASN* 1.3 59.5 + - - +
104C LEU* 3.3 6.4 + - - +
105C LEU* 2.9 31.0 + - - +
163C ARG* 2.9 36.1 + - - +
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Residues in contact with ASN 102 (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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98C PRO* 3.1 21.3 + - - +
99C PRO* 3.7 10.6 - - + +
100C ALA 3.2 0.2 - - - -
101C GLN* 1.3 78.1 - - - +
103C LEU* 1.3 62.2 + - + +
105C LEU* 3.8 8.0 - - - +
106C LYS* 3.0 41.3 + - - +
163C ARG* 3.1 26.8 + - - +
167C LEU* 4.6 9.2 - - + +
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Residues in contact with LEU 103 (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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19C ASN 3.4 22.7 - - - +
20C ALA 3.6 18.4 - - - +
21C THR 4.3 2.0 - - - -
22C TYR 3.9 20.0 - - - +
23C CYS* 3.9 21.7 - - + +
99C PRO 3.2 10.8 + - - +
100C ALA 3.4 5.6 + - - +
102C ASN* 1.3 75.9 - - + +
104C LEU* 1.3 55.3 + - - +
106C LYS* 3.9 12.3 - - + +
107C SER* 2.8 35.9 + - - -
112C GLU* 4.9 12.1 - - - +
411C PHE* 3.7 5.4 - - + -
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Residues in contact with LEU 104 (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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93C ILE* 3.8 37.5 - - + -
96C LEU* 3.6 25.1 - - + -
100C ALA 3.1 12.3 + - - +
101C GLN 3.4 9.2 - - - +
103C LEU* 1.3 75.9 - - - +
105C LEU* 1.3 65.5 + - + +
107C SER* 3.1 17.2 + - - -
108C TYR* 3.4 19.0 + - + -
384C ALA* 5.0 2.0 - - + -
402C ILE* 4.0 28.7 - - + -
404C VAL* 4.2 8.3 - - + -
411C PHE* 3.3 30.4 - - + -
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Residues in contact with LEU 105 (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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85C MET* 4.9 4.5 - - + -
93C ILE* 4.7 18.8 - - + -
101C GLN 2.9 16.6 + - - +
102C ASN* 3.4 4.5 + - - +
104C LEU* 1.3 79.0 - - + +
106C LYS* 1.3 55.7 + - - +
108C TYR* 3.6 1.1 + - + -
109C PHE* 2.9 58.2 + - + +
160C LEU* 4.2 24.0 - - + +
163C ARG* 3.7 52.5 - - + +
164C ALA* 4.7 2.2 - - + -
167C LEU* 3.5 20.9 - - + -
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Residues in contact with LYS 106 (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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102C ASN* 3.0 28.5 + - - +
103C LEU* 3.9 13.6 - - + +
105C LEU* 1.3 72.8 - - - +
107C SER* 1.3 68.7 + - - +
110C SER* 3.2 35.0 + - - +
112C GLU* 3.4 39.4 + - + +
113C GLY* 3.2 9.7 - - - -
167C LEU* 3.6 29.8 - - + -
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Residues in contact with SER 107 (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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23C CYS* 3.5 9.7 - - - -
24C ASP 4.6 2.3 + - - -
103C LEU 2.8 20.2 + - - -
104C LEU* 3.1 14.2 + - - -
106C LYS* 1.3 76.2 - - - +
108C TYR* 1.3 54.1 + - - +
113C GLY* 3.2 5.6 - - - -
114C ILE* 2.8 34.8 + - - +
402C ILE* 4.5 5.6 - - - -
411C PHE* 4.2 0.2 - - - -
413C LYS* 2.8 35.8 + - - +
417C PHE* 3.7 13.0 - - - -
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Residues in contact with TYR 108 (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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104C LEU* 3.4 17.2 + - + +
105C LEU* 4.1 1.6 - - + +
106C LYS 3.3 0.2 - - - -
107C SER* 1.3 80.3 - - - +
109C PHE* 1.3 75.2 + + + +
114C ILE* 3.6 4.1 - - + +
115C GLY 3.1 8.9 + - - -
116C TYR* 2.8 73.3 + + + +
380C ASP* 4.9 0.7 + - - -
383C LEU* 2.6 56.8 + - + -
401C PRO* 3.4 23.5 - - + +
402C ILE* 3.5 23.5 + - + -
417C PHE* 3.6 26.2 - + - -
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Residues in contact with PHE 109 (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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85C MET* 5.2 0.9 - - + -
105C LEU* 2.9 45.3 + - + +
108C TYR* 1.3 84.6 - + + +
110C SER* 1.3 61.9 + - - +
115C GLY* 4.2 7.7 - - - -
116C TYR* 3.6 42.9 - + + +
118C ILE 4.5 1.1 - - - -
119C ILE* 3.6 39.0 - - + -
164C ALA* 3.7 39.3 - - + +
167C LEU* 4.5 3.6 - - + -
168C ALA* 3.4 22.4 - - + +
169C GLN* 4.5 2.9 + - - +
172C VAL* 4.7 7.2 - - + -
383C LEU* 4.1 21.8 - - + -
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Residues in contact with SER 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LYS* 3.2 27.2 + - - +
109C PHE* 1.3 78.1 - - - +
111C GLU* 1.3 59.3 + - - +
112C GLU* 2.9 33.1 + - - +
113C GLY 2.9 24.9 + - - -
115C GLY 3.4 8.1 + - - -
167C LEU* 3.7 22.2 - - - +
168C ALA* 4.8 0.4 - - - +
169C GLN* 4.4 2.9 - - - -
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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