Contacts of the helix formed by residues 78 - 88 (chain B) in PDB entry 4K9N
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 ALA 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B GLU* 3.8 8.3 - - + +
48B ALA* 4.2 8.1 - - - +
51B VAL* 3.6 28.3 - - + -
69B LEU* 3.9 10.1 - - + -
74B GLY 3.4 8.7 + - - +
75B THR 3.0 11.5 + - - +
77B ASN* 1.3 76.3 - - - +
79B MET* 1.3 59.1 - - - +
80B GLY 3.3 2.9 - - - -
81B ALA* 3.1 8.1 + - - +
82B LEU* 3.0 30.8 + - + +
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Residues in contact with MET 79 (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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75B THR* 3.5 17.7 - - + +
76B GLY* 3.1 15.3 + - - +
77B ASN 3.4 0.6 - - - -
78B ALA* 1.3 79.0 - - - +
80B GLY* 1.3 62.3 + - - +
82B LEU* 3.3 20.3 + - - +
83B SER* 3.2 16.5 + - - -
118B LEU* 3.8 9.2 - - + +
119B PRO* 3.4 44.4 - - + +
122B LEU* 3.4 32.5 - - + +
76D GLY* 3.3 23.5 - - - +
79D MET* 4.2 9.6 - - + -
118D LEU* 3.6 16.6 - - + +
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Residues in contact with GLY 80 (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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78B ALA 3.3 0.6 - - - -
79B MET* 1.3 72.3 - - - +
81B ALA* 1.3 65.9 + - - +
83B SER* 3.0 20.0 + - - -
84B ASN* 3.5 10.8 + - - -
402B GLY* 6.1 0.4 - - - -
73D ALA* 3.6 25.2 - - - +
76D GLY* 3.3 10.6 - - - -
77D ASN* 3.3 22.1 + - - +
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Residues in contact with ALA 81 (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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48B ALA* 4.0 20.9 - - + +
51B VAL* 3.6 29.1 - - + +
52B GLY* 4.4 5.2 - - - +
55B ASP* 4.4 3.5 - - - +
78B ALA 3.1 12.6 + - - +
80B GLY* 1.3 75.9 - - - +
82B LEU* 1.3 63.4 + - - +
84B ASN* 3.3 12.2 + - - +
85B ALA* 3.1 21.0 + - - +
77D ASN* 4.2 3.6 + - - -
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Residues in contact with LEU 82 (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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51B VAL* 4.2 16.8 - - + -
69B LEU* 6.3 0.2 - - + -
75B THR* 5.2 5.4 - - + +
78B ALA* 3.0 21.4 + - + +
79B MET* 3.6 33.0 - - - +
80B GLY 3.2 0.4 - - - -
81B ALA* 1.3 77.1 - - - +
83B SER* 1.3 58.6 + - - +
85B ALA* 3.6 5.1 - - + +
86B TRP* 2.8 30.1 + - - +
92B LEU* 4.7 1.3 - - + -
94B VAL* 4.1 25.8 - - + -
119B PRO* 4.4 13.0 - - + -
122B LEU* 4.1 16.9 - - + +
123B VAL* 4.5 7.9 - - + -
153B PRO* 4.1 24.4 - - + +
155B TYR* 5.8 1.1 - - + -
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Residues in contact with SER 83 (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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79B MET 3.2 6.4 + - - -
80B GLY 3.0 16.5 + - - -
82B LEU* 1.3 79.6 - - - +
84B ASN* 1.3 62.1 + - - +
86B TRP* 3.5 3.8 + - - +
87B ASN* 3.3 15.4 + - - +
122B LEU* 3.7 30.2 - - - +
400B ALA* 3.5 19.1 - - - +
72D ALA* 4.7 10.5 - - - -
73D ALA* 3.7 25.8 + - - +
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Residues in contact with ASN 84 (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 ASP* 4.6 2.0 - - - +
80B GLY 3.5 9.2 + - - -
81B ALA* 3.3 11.6 + - - +
83B SER* 1.3 80.5 + - - +
85B ALA* 1.3 62.3 + - - +
87B ASN* 3.0 4.3 + - - -
88B SER* 3.0 23.6 + - - -
398B CYS* 3.5 9.1 - - - +
399B ALA* 3.6 9.5 - - - +
400B ALA* 2.9 27.6 + - - +
402B GLY* 2.8 45.0 + - - -
403B LEU 5.1 0.6 + - - -
404B GLY 5.5 0.4 - - - -
405B PHE* 3.6 28.4 - - + +
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Residues in contact with ALA 85 (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 ASP* 3.7 9.8 + - - +
81B ALA 3.1 13.7 + - - +
82B LEU* 3.2 11.0 + - - +
84B ASN* 1.3 77.2 - - - +
86B TRP* 1.3 61.6 + - - +
88B SER* 3.2 8.2 + - - -
89B HIS* 3.2 3.5 + - - -
90B SER* 3.0 29.4 + - - -
92B LEU* 3.7 29.4 - - + -
153B PRO* 3.8 14.3 - - + +
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Residues in contact with TRP 86 (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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82B LEU 2.8 16.7 + - - +
83B SER* 3.6 7.4 - - - +
84B ASN 3.2 0.2 - - - -
85B ALA* 1.3 77.7 - - - +
87B ASN* 1.3 79.4 + - - +
89B HIS* 3.3 21.4 + + - -
121B PRO 4.4 10.8 - - - -
122B LEU* 3.5 35.0 - - + +
123B VAL* 3.5 29.2 - - - -
124B LYS* 3.6 17.7 - - + -
151B GLN 5.2 0.2 - - - +
152B GLY* 5.6 0.9 - - - -
153B PRO* 4.0 13.3 - - + +
301B ASP* 5.8 2.0 - - - -
303B LEU* 4.0 28.3 - - + -
107D GLU* 5.4 5.5 + - - -
113D VAL* 6.0 5.5 - - + +
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Residues in contact with ASN 87 (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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83B SER 3.3 3.9 + - - +
84B ASN 3.0 4.0 + - - +
86B TRP* 1.3 97.1 + - - +
88B SER* 1.3 57.6 + - - +
89B HIS* 3.3 9.6 + - - -
209B PRO* 5.2 4.5 - - - +
238B PRO* 5.0 4.5 - - - +
279B ARG* 3.4 47.3 + - - +
304B GLU* 5.6 0.2 - - - +
399B ALA* 3.0 39.3 + - + +
400B ALA* 3.5 18.8 - - - +
109D LEU* 4.5 3.2 - - - +
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP* 4.1 0.3 + - - -
59B GLN* 3.7 25.9 + - - +
84B ASN 3.0 13.2 + - - -
85B ALA* 3.2 5.5 + - - -
86B TRP 3.3 0.2 - - - -
87B ASN* 1.3 76.3 - - - +
89B HIS* 1.3 70.5 + - - +
90B SER* 2.7 26.1 + - - -
209B PRO* 5.7 6.6 - - - +
210B ASP* 4.6 3.6 - - - +
213B ALA* 5.7 3.8 - - - +
238B PRO* 4.8 8.5 - - - -
239B ARG* 5.6 5.5 + - - -
399B ALA* 3.7 16.6 - - - -
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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