Contacts of the helix formed by residues 77 - 89 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B TYR* 4.8 2.2 - - - -
123B LYS* 2.5 48.3 + - + +
126B GLY 3.3 17.5 - - - +
127B GLY* 3.6 22.8 - - - +
128B ALA* 3.9 9.1 + - - +
73D ARG* 5.9 1.4 - - - +
74D ASP* 3.2 22.6 + - + +
75D PRO 3.1 3.6 - - - -
76D LEU* 1.3 75.2 - - - +
78D PHE* 1.3 58.7 + - - +
80D ALA* 3.3 10.0 + - + +
81D ASN* 2.8 39.7 + - - +
84D ARG* 4.8 6.1 + - - -
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Residues in contact with PHE 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLY* 3.7 4.0 + - - -
75D PRO 3.1 23.8 - - - -
76D LEU* 3.1 29.1 + - + -
77D GLU* 1.3 71.2 - - - +
79D ARG* 1.3 58.9 + - + +
81D ASN* 3.9 3.7 - - - +
82D TYR* 2.8 32.4 + - - +
106D ASP* 4.6 2.9 - - - +
109D LEU* 3.8 25.8 - - + -
110D TYR* 3.5 57.0 - + - +
113D ALA* 3.8 16.6 - - + -
124D LEU* 4.0 23.3 - - + -
290D THR* 3.6 10.9 + - + +
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Residues in contact with ARG 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ARG* 5.3 7.7 - - - +
125B MET 3.9 19.5 + - - -
126B GLY* 3.3 15.3 + - - +
129B GLN* 3.9 13.9 - - - +
293B LEU* 3.9 19.8 + - - +
296B MET* 4.0 20.5 - - - +
297B ASP* 2.5 44.7 + - - -
300B GLU* 5.7 0.2 + - - -
326B VAL* 5.4 1.1 - - + -
328B HIS* 6.1 1.6 - - - -
78D PHE* 1.3 79.9 - - + +
80D ALA* 1.3 58.5 + - - +
82D TYR* 3.7 0.5 - - - +
83D ASN* 2.9 39.8 + - - +
290D THR* 4.4 15.0 - - + -
294D ARG* 3.6 22.8 - - - +
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Residues in contact with ALA 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLY 2.9 17.7 + - - +
127B GLY* 3.9 9.6 - - - +
128B ALA 3.6 24.2 - - - +
129B GLN* 3.9 14.9 + - + +
77D GLU* 3.8 8.1 - - + +
79D ARG* 1.3 76.9 - - - +
81D ASN* 1.3 58.1 + - - +
83D ASN* 4.0 0.9 - - - +
84D ARG* 3.1 44.1 + - - +
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Residues in contact with ASN 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 5.0 1.6 - - - +
69D ALA 4.4 1.4 + - - -
70D VAL* 4.4 8.8 - - + +
73D ARG* 3.7 17.1 - - - +
74D ASP 3.0 23.0 + - - +
75D PRO* 3.9 9.5 - - - +
77D GLU* 2.8 29.4 + - - +
78D PHE* 3.9 3.1 - - - +
80D ALA* 1.3 70.1 - - - +
82D TYR* 1.3 65.3 + - - +
84D ARG* 3.0 28.2 + - - +
85D MET* 3.0 30.4 + - + +
109D LEU* 4.0 23.9 - - + +
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Residues in contact with TYR 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D PHE 2.8 21.9 + - - +
79D ARG 3.7 3.1 - - - +
81D ASN* 1.3 74.5 - - - +
83D ASN* 1.3 72.2 + - - +
85D MET* 3.4 10.9 + - - +
86D TYR* 3.0 47.3 + + + +
99D LEU* 3.7 21.3 - - - +
102D ILE* 3.7 18.8 - - + +
106D ASP* 4.3 7.3 + - - +
263D THR* 4.7 0.2 - - - +
264D ARG* 4.4 8.5 - - - -
287D GLY* 3.2 30.7 - - - -
290D THR* 3.8 25.8 - - + -
291D GLU* 3.4 38.2 + - + +
294D ARG* 6.4 0.9 - - - -
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Residues in contact with ASN 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLN* 2.8 39.4 + - - +
300B GLU* 5.8 0.2 + - - -
328B HIS* 3.9 18.4 + - - -
79D ARG* 2.9 24.5 + - - +
80D ALA 4.0 1.8 - - - +
82D TYR* 1.3 88.7 - - - +
84D ARG* 1.3 53.9 + - - +
86D TYR* 3.7 3.7 - - - +
87D ASP* 2.7 50.6 + - - +
264D ARG* 5.3 4.2 + - - -
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Residues in contact with ARG 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ALA 4.6 5.7 + - - -
68D GLU 5.3 0.2 - - - -
69D ALA* 3.0 38.2 + - + +
73D ARG* 3.5 49.0 - - - +
77D GLU* 4.8 5.3 + - - -
80D ALA* 3.1 39.0 + - - +
81D ASN* 3.0 26.1 - - - +
83D ASN* 1.3 73.8 - - - +
85D MET* 1.3 63.8 + - - +
87D ASP* 4.5 4.5 - - - -
88D THR* 2.8 43.3 + - + +
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Residues in contact with MET 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ILE* 4.1 16.4 - - + +
69D ALA* 3.6 13.0 - - + +
70D VAL* 3.9 20.9 - - + -
81D ASN 3.0 27.3 + - - +
82D TYR* 3.7 8.1 - - - +
84D ARG* 1.3 77.5 - - - +
86D TYR* 1.3 54.8 - - - +
88D THR* 3.6 0.4 + - - -
89D THR* 2.8 37.5 + - - +
102D ILE* 4.1 33.1 - - + +
105D ILE* 3.7 46.9 - - + -
106D ASP* 4.3 9.4 - - + +
109D LEU* 4.4 6.7 - - + -
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Residues in contact with TYR 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ASP* 2.5 30.2 + - - -
82D TYR* 3.0 43.1 + + + +
83D ASN* 3.7 4.9 - - - +
85D MET* 1.3 78.0 - - - +
87D ASP* 1.3 74.6 + - - +
89D THR* 3.5 1.9 + - - -
90D LYS* 3.1 39.8 + - + +
94D MET* 3.1 41.2 + - + +
95D ARG* 3.1 10.2 + - - -
99D LEU* 4.2 5.8 - - + -
102D ILE* 3.9 20.4 - - + -
263D THR* 4.3 10.1 - - + -
265D PHE* 3.6 8.9 - + - -
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Residues in contact with ASP 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D TRP* 3.6 23.0 - - + -
83D ASN* 2.7 36.9 + - - +
84D ARG* 4.0 4.2 - - - +
86D TYR* 1.3 80.7 - - - +
88D THR* 1.3 63.1 + - + +
89D THR 3.2 1.3 + - - -
90D LYS* 2.7 41.7 + - + +
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Residues in contact with THR 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LYS 4.2 7.0 - - - +
62D TRP 3.3 7.7 - - - -
64D ASN* 3.0 50.5 + - - +
65D ASN 5.2 1.6 + - - -
66D ILE 5.4 0.2 + - - -
69D ALA* 3.8 14.7 + - + +
84D ARG* 2.8 35.0 + - + +
85D MET 3.6 4.3 + - - -
87D ASP* 1.3 79.6 - - + +
89D THR* 1.3 61.3 + - - +
90D LYS 3.6 0.2 - - - -
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Residues in contact with THR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D PHE* 5.1 4.6 - - + -
62D TRP 3.3 3.4 - - - -
64D ASN 3.5 22.7 - - - +
66D ILE* 4.0 28.0 - - + +
85D MET 2.8 23.3 + - - +
86D TYR* 3.5 5.9 + - - -
87D ASP 3.2 0.2 - - - -
88D THR* 1.3 82.5 - - - +
90D LYS* 1.3 53.0 - - - +
91D TRP 2.9 4.7 + - - -
92D ILE* 3.0 17.8 + - + +
93D GLY* 2.7 37.6 + - - -
94D MET 5.2 0.3 + - - -
98D GLY 5.6 0.2 + - - -
102D ILE* 4.0 11.8 - - - +
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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