Contacts of the helix formed by residues 82 - 93 (chain t) in PDB entry 6QX2
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 GLY 82 (chain t).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122r ARG* 3.6 19.5 - - - +
81t HIS* 1.3 76.0 - - - +
83t ASP* 1.3 65.5 + - - -
84t SER* 3.3 3.8 - - - -
85t SER* 3.4 17.2 + - - -
86t ILE* 3.4 14.8 + - - +
8w C 2.9 19.8 + - - -
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Residues in contact with ASP 83 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83r ASP* 5.6 2.1 - - - +
121r MET* 6.1 4.7 - - + -
122r ARG* 3.2 26.7 + - - +
71t VAL* 3.9 8.4 - - + +
75t MET* 3.5 25.5 - - + +
81t HIS 3.7 1.6 + - - -
82t GLY* 1.3 67.4 - - - -
84t SER* 1.3 65.2 + - - +
86t ILE* 3.3 3.7 + - - +
87t TYR* 2.8 30.8 + - - +
121t MET* 3.8 25.4 - - + +
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Residues in contact with SER 84 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82t GLY* 3.3 1.4 - - - -
83t ASP* 1.3 86.1 + - - +
85t SER* 1.3 61.6 + - - +
87t TYR* 4.6 4.9 - - - +
88t GLU* 2.9 54.0 + - - +
121t MET* 5.2 1.1 - - - -
2009w G 6.1 0.7 - - - -
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Residues in contact with SER 85 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45t VAL* 4.3 1.4 - - - +
81t HIS* 5.1 0.7 - - - -
82t GLY* 3.4 13.7 + - - -
83t ASP 3.3 0.8 - - - -
84t SER* 1.3 78.0 + - - +
86t ILE* 1.3 63.4 + - - +
88t GLU* 4.5 4.0 - - - +
89t ALA* 3.4 21.5 + - - +
6w T 4.1 15.9 - - - +
7w A 3.4 59.0 + - - -
8w C 4.2 6.4 + - - -
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Residues in contact with ILE 86 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45t VAL* 4.1 7.9 - - + -
49t ILE* 3.5 23.0 - - + +
70t ILE* 6.4 0.4 - - + -
71t VAL* 3.9 26.5 - - + +
74t VAL* 4.1 9.0 - - + -
75t MET* 3.7 34.3 - - + +
79t HIS* 3.6 40.6 - - + +
81t HIS 4.2 1.6 - - - +
82t GLY 3.4 15.0 + - - +
83t ASP 3.3 5.5 + - - +
84t SER 3.2 0.6 - - - -
85t SER* 1.3 73.9 - - - +
87t TYR* 1.3 66.7 + - - +
89t ALA* 3.2 5.4 + - - +
90t MET* 3.0 19.4 + - + +
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Residues in contact with TYR 87 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67t SER* 3.6 13.0 - - - -
71t VAL* 4.1 11.4 - - + -
83t ASP 2.8 20.5 + - - +
84t SER* 4.2 4.0 - - - +
86t ILE* 1.3 73.4 - - - +
88t GLU* 1.3 62.9 + - + +
90t MET* 3.1 22.5 + - + +
91t VAL* 2.8 52.3 + - + +
110t PHE* 4.7 1.1 - + - -
118t ALA* 4.0 7.4 - - + +
119t ALA 2.8 28.6 + - - -
120t ALA* 3.8 2.5 + - - -
121t MET* 3.6 40.4 - - + -
124t THR* 2.7 35.5 + - - +
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Residues in contact with GLU 88 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84t SER* 2.9 38.7 + - - +
85t SER* 4.5 3.6 - - - +
87t TYR* 1.3 82.1 - - + +
89t ALA* 1.3 57.0 + - - +
91t VAL* 3.4 11.1 + - + +
92t ARG* 3.1 31.4 + - - +
6w T 4.0 22.9 - - + +
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Residues in contact with ALA 89 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45t VAL* 4.0 23.6 - - + -
46t HIS* 3.9 8.1 - - - +
49t ILE* 4.0 7.2 - - + -
85t SER 3.4 18.8 + - - +
86t ILE 3.2 5.7 + - - +
88t GLU* 1.3 76.7 - - - +
90t MET* 1.3 62.5 + - - +
92t ARG* 3.8 3.8 + - - +
93t MET* 3.4 28.2 + - - +
6w T 3.8 22.2 - - - +
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Residues in contact with MET 90 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49t ILE* 3.9 21.9 - - + +
53t LEU* 5.4 2.0 - - - -
67t SER* 3.5 29.2 - - - +
70t ILE* 4.1 27.1 - - - -
71t VAL* 5.2 4.7 - - + -
86t ILE* 3.0 13.7 + - + +
87t TYR* 3.4 28.3 - - + +
89t ALA* 1.3 74.9 - - - +
91t VAL* 1.3 65.9 + - - +
93t MET* 3.2 22.6 + - - +
94t ALA* 3.4 10.6 + - - +
104t VAL* 4.1 14.4 - - + +
110t PHE* 4.3 10.8 - - + -
126t ALA* 3.9 21.3 - - + -
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Residues in contact with VAL 91 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87t TYR* 2.8 46.1 + - + +
88t GLU* 3.4 11.0 + - + +
90t MET* 1.3 74.3 - - - +
92t ARG* 1.3 54.9 + - + +
94t ALA* 2.8 28.4 + - - +
95t GLN* 3.3 32.2 + - - +
110t PHE* 3.8 20.5 - - + +
118t ALA* 3.6 35.9 - - + +
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Residues in contact with ARG 92 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46t HIS* 5.5 1.3 + - - +
88t GLU 3.1 13.8 + - - +
89t ALA* 3.9 6.5 - - - +
91t VAL* 1.3 79.1 - - + +
93t MET* 1.3 58.3 + - - +
94t ALA 3.0 4.6 + - - -
95t GLN* 3.1 33.5 + - - +
98t SER* 3.6 29.3 + - - +
99t TYR* 3.1 36.5 + - + -
172t ALA* 5.8 3.2 - - - +
173t SER* 5.1 7.9 + - - +
266t PHE* 5.8 2.6 - - - -
267t GLN* 4.9 8.3 - - - +
5w G 2.6 56.8 + - - +
6w T 4.0 27.7 + - - +
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Residues in contact with MET 93 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46t HIS* 3.9 24.7 - - + +
49t ILE* 3.6 41.3 - - + -
50t LEU* 4.1 18.2 - - + -
89t ALA 3.4 19.5 + - - +
90t MET* 3.2 13.9 + - - +
92t ARG* 1.3 75.7 - - - +
94t ALA* 1.3 55.6 + - - +
95t GLN 3.5 0.4 - - - -
99t TYR* 3.5 31.4 - - + +
102t PRO* 3.4 8.5 - - - +
103t LEU* 3.0 42.6 + - + -
104t VAL* 3.2 16.5 + - + -
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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