Contacts of the helix formed by residues 77 - 88 (chain X) in PDB entry 3MQT
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 GLU 77 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122T TYR* 3.5 12.5 - - - -
123T LYS* 3.2 41.8 + - + +
126T GLY 3.3 15.7 - - - +
127T GLY* 3.6 17.0 - - - -
128T ALA* 3.9 12.4 + - - +
73X ARG* 5.7 2.1 - - - +
74X ASP* 3.2 21.3 + - + +
75X PRO 3.1 3.0 - - - -
76X LEU* 1.3 74.3 - - - +
78X PHE* 1.3 64.6 + - - +
80X ALA* 3.3 10.1 + - + +
81X ASN* 2.9 29.3 + - - +
84X ARG* 4.5 7.3 + - - -
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Residues in contact with PHE 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126T GLY* 3.6 6.0 + - - -
75X PRO 3.2 23.1 - - - -
76X LEU* 3.0 31.7 + - + -
77X GLU* 1.3 72.3 - - - +
79X ARG* 1.3 59.3 + - + +
81X ASN* 3.8 3.6 - - - +
82X TYR* 2.8 32.9 + - - +
106X ASP* 4.7 3.2 - - - +
109X LEU* 3.9 9.6 - - + +
110X TYR* 3.5 74.9 - + - +
113X ALA* 3.9 15.3 - - + -
124X LEU* 4.1 23.8 - - + -
290X THR* 3.5 11.1 + - + +
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Residues in contact with ARG 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79T ARG* 4.9 11.3 - - - +
125T MET 3.7 21.4 + - - -
126T GLY* 3.3 13.2 + - - +
129T GLN* 4.0 11.9 - - - +
293T LEU* 4.1 17.4 + - - +
296T MET* 3.8 20.7 - - - +
297T ASP* 2.6 44.3 + - - -
326T VAL* 5.2 0.9 - - - -
328T HIS* 6.0 2.6 - - - -
78X PHE* 1.3 79.7 - - + +
80X ALA* 1.3 58.4 + - - +
82X TYR* 3.8 0.8 - - - +
83X ASN* 2.8 43.9 + - - +
290X THR* 4.3 15.9 - - + -
294X ARG* 4.1 21.0 - - - +
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Residues in contact with ALA 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126T GLY 3.0 16.2 + - - +
127T GLY 4.0 6.1 - - - -
128T ALA 3.6 14.1 - - - +
129T GLN* 3.6 31.7 - - + +
77X GLU* 3.9 10.5 - - + +
79X ARG* 1.3 75.7 - - - +
81X ASN* 1.3 58.2 + - - +
83X ASN* 3.5 1.6 + - - +
84X ARG* 2.9 43.8 + - - +
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Residues in contact with ASN 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X ILE* 5.1 1.0 - - - +
69X ALA 4.3 1.6 + - - -
70X VAL* 4.2 16.8 - - + +
73X ARG* 3.7 17.9 - - - +
74X ASP 2.9 25.8 + - - +
75X PRO* 4.1 6.2 - - - +
77X GLU* 2.9 25.0 + - - +
78X PHE 3.8 2.5 - - - +
80X ALA* 1.3 75.6 - - - +
82X TYR* 1.3 56.1 + - - +
84X ARG* 2.7 37.6 + - - +
85X MET* 2.8 41.3 + - - +
109X LEU* 4.2 16.4 - - + +
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Residues in contact with TYR 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78X PHE 2.8 21.6 + - - +
79X ARG* 3.8 2.9 - - - +
81X ASN* 1.3 70.5 - - - +
83X ASN* 1.3 75.5 + - - +
85X MET* 3.3 12.1 + - - +
86X TYR* 2.9 46.3 + + + +
99X LEU* 3.5 21.8 - - - +
102X ILE* 3.7 21.7 - - + +
106X ASP* 4.3 6.9 + - + +
263X THR* 4.8 0.2 - - - +
264X ARG* 4.7 6.1 - - - -
287X GLY* 3.1 29.4 - - - -
290X THR* 4.0 25.4 - - + -
291X GLU* 3.4 37.8 + - + +
294X ARG* 6.1 2.0 - - - -
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Residues in contact with ASN 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129T GLN* 2.7 34.3 + - - +
328T HIS* 3.8 19.3 + - - -
79X ARG* 2.8 28.5 + - - +
80X ALA 3.9 1.8 - - - +
82X TYR* 1.3 88.3 - - - +
84X ARG* 1.3 57.8 + - - +
86X TYR* 3.8 3.9 - - - +
87X ASP* 2.8 45.5 + - - +
264X ARG* 5.2 6.2 + - - -
294X ARG* 5.8 1.4 + - - -
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Residues in contact with ARG 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128T ALA 4.4 7.3 + - - -
68X GLU 5.3 0.4 - - - -
69X ALA* 2.9 34.6 + - + +
73X ARG* 3.4 45.7 - - - +
77X GLU* 4.5 5.1 + - - -
80X ALA* 2.9 40.4 + - - +
81X ASN* 2.7 32.9 - - - +
82X TYR 3.1 0.2 - - - -
83X ASN* 1.3 74.3 - - - +
85X MET* 1.3 64.9 + - - +
87X ASP* 4.6 3.1 - - + -
88X THR* 2.8 43.2 + - + +
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Residues in contact with MET 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66X ILE* 3.9 17.5 - - + +
69X ALA* 3.7 19.0 - - + +
70X VAL* 3.9 11.9 - - + -
81X ASN 2.8 27.1 + - - +
82X TYR* 3.7 14.6 - - - +
84X ARG* 1.3 73.7 - - - +
86X TYR* 1.3 54.3 + - - +
88X THR* 3.5 0.6 + - - -
89X THR* 2.6 37.4 + - - +
102X ILE* 4.0 34.3 - - + +
105X ILE* 3.7 44.4 - - + -
106X ASP* 4.4 9.4 - - + +
109X LEU* 4.6 7.9 - - + -
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Residues in contact with TYR 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239P ASP* 2.5 29.6 + - - -
82X TYR* 2.9 42.4 + + + +
83X ASN* 3.8 4.9 - - - +
85X MET* 1.3 78.4 - - - +
87X ASP* 1.3 67.4 + - - +
89X THR* 3.3 2.4 + - - -
90X LYS* 3.1 52.0 + - + +
94X MET* 3.1 35.0 + - + +
95X ARG* 3.1 20.1 + - - -
99X LEU* 4.3 8.1 - - + -
102X ILE* 3.8 12.5 - - + +
263X THR* 4.2 11.9 - - + -
265X PHE* 3.7 9.2 - + - -
291X GLU* 6.0 0.2 - - - -
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Residues in contact with ASP 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237P GLN* 5.7 2.0 + - - -
61X LYS 4.3 0.4 - - - +
62X TRP* 3.5 17.1 - - + -
83X ASN* 2.8 36.9 + - - +
84X ARG* 4.1 4.2 - - - +
86X TYR* 1.3 80.0 - - - +
88X THR* 1.3 63.6 + - + +
89X THR 3.2 1.2 + - - -
90X LYS* 3.0 40.6 + - + +
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Residues in contact with THR 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X LYS 4.0 10.1 - - - +
62X TRP 3.4 6.5 - - - -
64X ASN* 2.9 49.8 + - + +
65X ASN 5.2 1.9 + - - -
66X ILE 5.3 0.5 + - - -
69X ALA* 3.8 15.1 + - + +
84X ARG* 2.8 36.1 + - + +
85X MET* 3.5 5.9 + - - -
87X ASP* 1.3 78.9 - - + +
89X THR* 1.3 61.4 + - - +
90X LYS 3.7 0.2 - - - -
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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
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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