Contacts of the helix formed by residues 50 - 59 (chain B) in PDB entry 3AQQ
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 THR 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLU* 3.5 15.7 - - - +
48B THR 3.3 5.8 + - - +
49B ARG* 1.3 77.7 - - - +
51B PHE* 1.3 66.9 + - - +
52B SER* 3.1 8.3 + - - -
53B ALA* 3.4 21.0 + - + +
54B THR* 2.9 17.3 + - - -
115B PRO* 4.9 18.4 - - + -
61C PRO* 4.8 4.5 - - - +
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLY* 5.7 1.6 - - - -
98A GLU* 3.0 14.3 + - - +
99A TYR* 3.8 28.7 - + + -
128A ILE* 3.7 26.9 - - + +
129A THR 3.3 26.0 - - - -
130A HIS* 4.6 0.9 - - - -
131A LEU* 3.5 44.2 - - + -
49B ARG 3.5 1.1 + - - -
50B THR* 1.3 72.8 - - - +
52B SER* 1.3 65.9 + - - +
54B THR* 3.3 7.1 - - - -
55B VAL* 2.9 38.1 + - + +
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 3.2 5.8 + - - -
51B PHE* 1.3 83.7 - - - +
53B ALA* 1.3 62.1 + - - +
54B THR 3.1 1.6 - - - -
55B VAL* 3.4 10.8 - - - +
56B ARG* 2.7 35.0 + - - +
61C PRO* 3.7 20.3 - - - +
62C VAL 4.9 10.2 + - - -
63C TYR* 5.4 3.5 - - - -
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ARG* 3.8 15.5 - - + -
50B THR* 3.3 22.9 + - + +
52B SER* 1.3 76.8 + - - +
54B THR* 1.3 65.1 + - - +
56B ARG* 3.5 11.5 - - - +
57B ALA* 2.9 26.5 + - - +
112B CYS* 4.2 15.1 - - - -
113B SER 4.8 5.8 - - - +
115B PRO* 4.9 4.7 - - + -
60C GLY* 6.3 0.2 - - - -
61C PRO* 4.3 16.0 - - + +
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Residues in contact with THR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 3.8 33.0 - - + +
97A GLY* 3.4 8.6 - - - +
127A VAL* 3.9 21.9 - - + +
128A ILE 5.6 0.7 - - - +
49B ARG* 3.1 30.2 + - - +
50B THR 2.9 12.5 + - - -
51B PHE* 3.3 9.9 - - - -
53B ALA* 1.3 79.7 - - - +
55B VAL* 1.3 64.7 + - - +
57B ALA* 3.9 2.2 - - - +
58B SER* 3.2 21.0 + - - -
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A VAL* 4.3 4.0 - - + -
128A ILE 3.7 20.9 - - - +
129A THR* 4.9 19.7 - - + +
51B PHE* 2.9 35.0 - - + +
52B SER* 3.0 14.1 + - - +
54B THR* 1.3 76.5 - - - +
56B ARG* 1.3 64.6 + - - +
58B SER* 2.8 25.9 + - - +
59B GLN* 3.2 13.5 + - + +
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B SER 2.7 24.0 + - - +
53B ALA* 3.5 8.5 - - - +
55B VAL* 1.3 75.9 - - + +
57B ALA* 1.3 79.2 + - - +
59B GLN* 3.3 15.8 + - - +
60B GLY* 3.3 11.7 + - - -
61B PRO* 6.1 0.2 - - - +
111B MET 4.9 0.6 + - - -
112B CYS* 4.9 2.9 - - - -
58C SER 3.7 13.4 + - - -
59C GLN* 3.4 38.6 + - - +
60C GLY* 2.6 37.1 + - - +
61C PRO* 3.9 10.8 - - + -
62C VAL* 4.7 9.1 - - + +
110C LYS* 3.4 19.4 - - - +
62D VAL* 4.5 20.4 - - - +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ARG* 5.3 1.3 - - - -
53B ALA 2.9 18.3 + - - +
54B THR* 3.9 5.4 - - - +
56B ARG* 1.3 83.1 - - - +
58B SER* 1.3 57.7 - - - +
60B GLY* 2.8 22.3 + - - -
110B LYS* 3.3 16.2 - - - +
111B MET 3.7 8.3 - - - +
112B CYS* 3.6 24.7 - - + -
124B VAL* 3.7 18.2 - - + -
125B GLU* 4.8 0.2 - - - -
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A THR* 4.8 4.2 + - - -
127A VAL* 3.6 25.6 - - - +
129A THR* 5.9 0.9 - - - +
54B THR 3.2 13.4 + - - -
55B VAL* 2.8 16.5 + - - +
57B ALA* 1.3 78.8 - - - +
59B GLN* 1.3 58.9 + - - +
60B GLY 4.2 0.2 - - - +
110B LYS* 2.8 24.8 + - - -
125B GLU* 3.2 28.1 + - - -
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Residues in contact with GLN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B VAL* 3.2 17.5 + - + +
56B ARG* 3.3 10.8 + - - +
57B ALA 2.9 2.0 + - - -
58B SER* 1.3 81.4 + - - +
60B GLY* 1.3 61.5 + - - +
59D GLN 4.8 6.0 + - - +
60D GLY 4.6 7.7 + - - +
61D PRO* 4.4 28.7 - - + +
62D VAL* 4.2 21.6 + - + +
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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