Contacts of the helix formed by residues 67 - 78 (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 SER 67 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65T LYS 3.6 0.6 + - - -
66T LYS* 1.3 68.2 - - - +
68T ALA* 1.3 56.8 + - - +
70T ILE* 2.9 14.0 + - - +
71T VAL* 2.8 39.4 + - - +
87T TYR* 3.6 17.9 - - - -
90T MET* 3.6 17.0 - - - +
121T MET* 3.5 8.1 - - - -
124T THR* 2.6 41.5 + - - -
125T GLU* 3.7 7.1 + - - -
126T ALA* 4.3 0.3 - - - +
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Residues in contact with ALA 68 (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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68R ALA 4.3 1.0 - - - +
72R GLY* 3.3 12.5 - - - -
75R MET* 3.3 43.7 - - + -
66T LYS* 3.3 2.2 - - + -
67T SER* 1.3 77.5 - - - +
69T ARG* 1.3 55.6 + - - +
71T VAL* 4.3 0.5 - - - +
72T GLY* 3.1 22.3 + - - -
121T MET* 3.4 39.3 + - + +
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Residues in contact with ARG 69 (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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69R ARG 5.3 0.7 - - - +
72R GLY* 3.4 28.4 + - - +
73R ASP* 4.5 6.5 + - - +
76R GLY* 4.5 14.4 - - - -
77R LYS* 5.0 17.9 - - - +
58T MET* 5.5 5.6 - - + -
65T LYS* 4.4 20.6 - - + -
66T LYS* 3.2 19.4 + - + +
67T SER 3.1 0.4 - - - -
68T ALA* 1.3 76.5 - - - +
70T ILE* 1.3 59.4 + - + +
72T GLY* 3.9 0.5 - - - -
73T ASP* 3.1 29.0 + - + +
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Residues in contact with ILE 70 (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* 5.0 3.8 - - + +
52T GLY 5.7 0.2 - - - -
53T LEU* 3.7 31.0 - - + +
58T MET* 3.6 28.5 - - + -
65T LYS* 3.9 8.3 - - + +
66T LYS 3.6 8.1 - - - +
67T SER* 2.9 9.9 + - - +
69T ARG* 1.3 74.7 - - + +
71T VAL* 1.3 59.8 + - - +
73T ASP* 3.3 7.7 + - - +
74T VAL* 3.0 40.8 + - + +
86T ILE* 6.4 0.4 - - + -
90T MET* 4.1 16.8 - - - -
126T ALA* 3.7 38.8 - - + +
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Residues in contact with VAL 71 (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 2.8 22.2 + - - +
68T ALA 4.3 0.7 - - - +
70T ILE* 1.3 68.5 - - - +
72T GLY* 1.3 58.7 + - - +
74T VAL* 3.4 1.6 + - - +
75T MET* 2.9 34.1 + - + +
83T ASP* 3.9 38.4 - - + +
86T ILE* 3.9 20.9 - - + +
87T TYR* 4.1 29.8 - - + -
90T MET* 4.9 8.5 - - - -
121T MET* 4.0 22.0 - - + -
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Residues in contact with GLY 72 (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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68R ALA* 3.3 35.2 - - - -
69R ARG* 3.5 18.3 + - - +
68T ALA 3.1 13.7 + - - -
69T ARG 3.9 0.9 - - - -
71T VAL* 1.3 76.7 - - - +
73T ASP* 1.3 51.7 - - - +
75T MET* 3.8 1.6 - - - +
76T GLY 2.9 29.1 + - - -
121T MET* 6.0 0.2 - - - +
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Residues in contact with ASP 73 (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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69R ARG* 4.3 12.7 + - + +
52T GLY* 3.8 18.2 - - - +
56T GLN* 3.5 29.8 + - + +
58T MET* 5.0 1.6 - - - +
69T ARG* 3.1 18.8 + - + +
70T ILE* 3.3 7.2 + - - +
72T GLY* 1.3 73.7 - - - +
74T VAL* 1.3 64.3 + - - +
76T GLY* 3.5 1.0 + - - -
77T LYS* 2.8 68.7 + - - +
78T TYR* 4.6 2.0 - - - -
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Residues in contact with VAL 74 (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 5.2 0.4 - - - +
48T ARG* 3.9 33.4 - - + +
49T ILE* 3.9 18.2 - - + +
52T GLY* 4.4 12.8 - - - -
70T ILE* 3.0 28.9 + - + +
71T VAL* 3.9 3.4 - - - +
73T ASP* 1.3 76.0 - - - +
75T MET* 1.3 58.6 + - - +
78T TYR* 3.0 19.7 + - + -
79T HIS* 3.0 40.9 + - + -
86T ILE* 4.2 18.8 - - + -
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Residues in contact with MET 75 (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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66R LYS* 4.4 16.2 - - + +
68R ALA* 3.3 25.4 - - + -
122R ARG* 3.8 28.7 - - + +
71T VAL* 2.9 24.3 + - + +
72T GLY 3.8 2.2 - - - +
74T VAL* 1.3 75.1 - - - +
76T GLY* 1.3 65.6 + - - +
79T HIS 3.3 24.6 + - - +
80T PRO* 4.0 3.6 - - + +
81T HIS 3.2 26.2 - - - +
83T ASP* 3.5 33.4 - - + -
86T ILE* 3.7 7.2 - - + -
121T MET* 5.7 0.7 - - + -
150T TYR* 3.8 7.6 + - - -
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Residues in contact with GLY 76 (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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66R LYS* 4.1 18.5 - - - +
69R ARG* 3.9 14.8 - - - -
72T GLY 2.9 17.0 + - - -
73T ASP 3.9 1.8 - - - -
74T VAL 3.3 0.2 - - - -
75T MET* 1.3 77.4 - - - +
77T LYS* 1.3 58.1 + - - +
150T TYR* 2.6 24.2 + - - -
151T ASP* 4.5 3.5 - - - +
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Residues in contact with LYS 77 (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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69R ARG* 3.0 39.1 - - - +
56T GLN* 3.4 19.6 + - - +
73T ASP* 2.8 39.9 + - - +
76T GLY* 1.3 76.6 - - - +
78T TYR* 1.3 93.2 + - + +
149T ASN* 2.9 29.6 + - - +
150T TYR* 3.9 4.0 - - - -
154T GLU* 3.8 30.2 - - + +
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Residues in contact with TYR 78 (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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48T ARG* 3.3 57.3 + - + -
51T TYR* 3.6 21.8 - + - -
52T GLY* 4.0 20.9 - - - -
55T GLU* 3.6 26.5 - - - +
56T GLN* 5.2 0.5 + - - -
73T ASP* 4.6 5.8 - - - -
74T VAL* 3.0 15.5 + - - +
76T GLY 3.8 0.6 - - - -
77T LYS* 1.3 116.0 + - + +
79T HIS* 1.3 59.9 + - - +
80T PRO* 3.4 9.3 - - - +
149T ASN* 4.6 3.4 - - + -
150T TYR* 3.8 10.0 + - - +
154T GLU* 4.6 9.3 + - + -
155T ARG 4.0 9.6 - - - -
156T GLU* 4.0 22.9 - - + +
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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