Contacts of the helix formed by residues 53 - 61 (chain B) in PDB entry 5NC5
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 ASP 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A GLN* 5.1 0.5 - - - +
214A VAL 4.5 5.2 - - - +
215A ALA* 5.3 0.7 - - - -
217A GLY 5.9 0.7 - - - +
233A SER* 4.0 11.4 - - - +
234A ILE 4.9 5.1 - - - +
235A ILE* 3.7 39.6 - - + +
238A THR* 6.1 0.3 - - - +
52B ALA* 1.3 76.2 - - - +
54B ALA* 1.3 69.2 + - - +
55B LYS* 2.8 25.3 + - - +
56B THR* 2.3 46.3 + - - -
57B VAL* 3.0 9.6 + - - +
83B ASP 4.1 3.8 - - - -
84B SER* 4.2 7.9 - - - +
726B GLN* 5.5 0.3 - - - +
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Residues in contact with ALA 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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53B ASP* 1.3 73.6 - - - +
55B LYS* 1.3 57.7 + - - +
57B VAL* 3.3 2.9 + - - +
58B GLN* 2.9 29.3 + - - +
82B SER* 3.5 23.6 - - - +
83B ASP* 3.5 20.4 - - - -
84B SER* 3.6 12.0 + - - +
813B SER 3.7 21.4 + - - +
814B PRO 4.0 4.9 - - - -
815B ARG 4.1 0.7 - - - +
816B LEU* 3.8 11.9 - - + -
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLN* 4.6 3.1 - - - +
235A ILE* 6.2 2.0 - - + -
238A THR* 4.5 21.8 - - + -
53B ASP* 2.8 12.0 + - - +
54B ALA* 1.3 79.9 - - - +
56B THR* 1.3 56.7 + - - +
58B GLN* 3.6 1.3 - - - +
59B ASP* 2.8 52.1 + - - +
692B HIS* 5.8 5.1 - - - +
726B GLN* 6.4 0.4 - - - +
813B SER 5.2 1.2 + - - +
816B LEU* 3.6 23.4 - - + +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLN* 3.0 50.4 + - + +
214A VAL 4.1 12.9 + - - -
237A GLN 5.2 0.2 + - - -
49B TYR* 4.0 21.1 - - + -
52B ALA* 4.4 6.5 - - + -
53B ASP* 2.3 33.0 + - - -
55B LYS* 1.3 76.1 - - - +
57B VAL* 1.3 66.3 + - - +
60B THR* 3.0 29.9 + - + +
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Residues in contact with VAL 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 TYR* 4.1 11.0 - - + -
52B ALA* 3.7 24.2 - - + -
53B ASP 3.0 10.8 + - - +
54B ALA 3.7 6.7 - - - +
56B THR* 1.3 74.3 - - - +
58B GLN* 1.3 66.0 + - - +
60B THR* 4.5 3.1 - - - -
61B VAL* 2.9 28.2 + - + +
62B THR* 3.1 7.5 + - - +
82B SER* 3.7 12.1 - - - -
83B ASP 4.4 2.9 - - - +
86B GLY* 3.9 22.9 - - - -
87B THR 4.2 5.2 - - - +
88B VAL* 3.7 33.7 - - + -
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Residues in contact with GLN 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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54B ALA 2.9 17.6 + - - +
55B LYS* 3.6 7.0 - - - +
56B THR 3.2 0.2 - - - -
57B VAL* 1.3 79.5 - - - +
59B ASP* 1.3 70.4 + - - +
62B THR* 3.2 12.2 + - - -
63B GLN* 2.9 40.6 + - + +
80B SER* 5.2 0.3 + - - -
82B SER* 3.8 8.3 + - - +
816B LEU* 3.3 41.4 - - + +
817B GLU 4.8 1.4 + - - -
818B ARG* 3.2 48.4 - - - +
823B PRO* 4.8 5.7 - - - +
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Residues in contact with ASP 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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213A GLN* 3.5 21.9 + - - +
239A ARG* 5.1 4.0 + - + -
763A ILE* 3.2 33.8 - - + +
766A GLY* 6.0 0.2 - - - -
768A VAL* 3.5 27.6 - - - +
55B LYS* 2.8 42.4 + - - +
56B THR 4.3 1.1 - - - +
58B GLN* 1.3 81.7 + - - +
60B THR* 1.4 60.5 + - + +
63B GLN* 3.5 20.2 + - - +
64B VAL* 5.0 0.9 - - - +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLN* 3.7 34.3 - - + +
239A ARG* 4.7 15.9 - - - +
49B TYR* 3.9 5.7 - - + -
56B THR* 3.0 23.3 + - + +
59B ASP* 1.4 80.8 - - + +
61B VAL* 1.3 70.1 + - - +
64B VAL* 3.5 19.7 - - - +
117B LEU 4.3 2.8 - - - +
118B LEU* 4.4 0.9 - - - +
119B PRO* 3.5 33.0 - - + +
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Residues in contact with VAL 61 (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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47B ALA* 4.3 10.1 - - + -
49B TYR* 4.4 6.3 - - + -
57B VAL* 2.9 18.4 + - + +
60B THR* 1.3 94.4 - - - +
62B THR* 1.3 67.1 + - - +
63B GLN 3.3 0.4 - - - -
64B VAL* 3.1 4.1 + - - +
65B ILE* 2.9 43.7 + - + +
88B VAL* 3.9 23.6 - - + -
118B LEU* 4.3 7.0 - - + -
119B PRO* 4.1 4.0 - - + -
122B VAL* 3.8 35.4 - - + -
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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