Contacts of the helix formed by residues 70 - 75 (chain K) in PDB entry 3J7Y
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 ASN 70 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K SER 3.6 0.2 + - - -
69K GLY* 1.3 70.8 - - - -
71K LYS* 1.3 59.3 + - - +
72K TRP* 3.3 3.1 - - - -
73K GLU* 3.2 7.9 + - + +
74K GLN* 2.9 43.0 + - + +
149r ARG* 5.0 4.8 - - - +
152r THR* 3.6 12.2 - - - +
153r ARG 3.8 3.8 + - - -
154r TRP* 3.0 59.8 + - + +
155r ALA 4.0 0.6 + - - -
156r PRO* 3.8 21.0 - - - +
159r VAL* 4.0 9.3 - - + +
174r MET* 5.7 1.5 - - - +
175r PRO* 3.9 11.3 + - + +
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Residues in contact with LYS 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2240A C 2.9 34.9 + - - +
2241A A 4.0 1.0 + - - -
27K PRO* 6.2 0.2 - - - +
67K PHE* 3.5 30.7 - - + -
68K SER* 2.6 40.1 + - - +
69K GLY 3.3 4.6 + - - -
70K ASN* 1.3 76.5 - - - +
72K TRP* 1.3 60.1 + - - +
74K GLN* 4.3 2.5 - - - -
75K LYS* 2.8 44.3 + - + +
92K ALA* 3.8 2.2 - - - +
174r MET* 3.6 26.0 - - + -
176r VAL* 3.8 13.0 - - + -
196r HIS* 3.4 25.4 + - - -
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Residues in contact with TRP 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65K ILE* 3.7 26.7 - - + -
67K PHE* 3.6 40.5 - + + +
69K GLY 5.0 0.2 + - - -
70K ASN 3.2 0.8 + - - -
71K LYS* 1.3 78.7 - - - +
73K GLU* 1.3 60.1 + - + +
91K THR* 4.1 2.1 - - - -
92K ALA* 3.6 8.8 + - + -
93K ALA* 3.2 44.5 + - - +
96K HIS* 3.5 39.9 - + + -
103K ILE* 3.5 24.0 - - + -
147r LEU* 3.6 32.3 - - + +
148r ASN 2.6 28.8 + - - -
149r ARG* 3.7 31.9 - - - +
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Residues in contact with GLU 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K ASN* 3.2 8.1 + - + +
71K LYS 3.2 0.2 - - - -
72K TRP* 1.3 78.3 - - + +
74K GLN* 1.3 62.6 + - - +
75K LYS 3.7 0.2 - - - -
91K THR* 3.7 12.2 - - - +
93K ALA* 5.6 0.7 - - - -
147r LEU* 5.9 3.2 - - + +
149r ARG* 4.3 12.0 + - - +
156r PRO* 3.2 46.1 - - + +
157r GLY* 4.1 3.8 + - - -
159r VAL* 4.0 19.4 - - + +
161r PRO* 3.5 23.4 - - - +
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Residues in contact with GLN 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K ASN* 2.9 22.3 + - + +
73K GLU* 1.3 79.1 - - - +
75K LYS* 1.3 63.4 + - - +
76K VAL 3.4 1.6 + - - -
154r TRP* 4.9 2.6 - - - +
159r VAL* 3.0 37.3 - - + +
160r LYS 4.1 9.9 + - - +
161r PRO* 3.7 5.2 - - - +
162r ILE* 2.8 44.3 + - + +
172r VAL* 6.1 0.8 - - - +
173r ARG 4.5 0.8 + - - +
174r MET* 3.2 40.1 - - + +
175r PRO* 3.3 15.8 - - - +
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Residues in contact with LYS 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2238A A 5.4 0.4 - - - -
2239A A 2.8 50.4 + - - -
2240A C 5.0 2.0 - - - -
67K PHE* 4.1 23.1 - - + -
71K LYS* 2.8 27.5 + - + +
74K GLN* 1.3 70.5 - - - +
76K VAL* 1.3 63.0 + - - +
77K TYR* 3.4 37.3 + - + +
91K THR* 3.5 2.9 - - - -
92K ALA* 2.8 34.2 + - + +
162r ILE* 5.6 0.2 - - - -
174r MET* 3.9 31.1 - - + +
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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