Contacts of the helix formed by residues 85 - 95 (chain K) in PDB entry 5XVO
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 85 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1K MET* 4.2 15.0 - - + +
83K ARG 4.3 3.8 - - - +
84K HIS* 1.3 82.8 - - + +
86K SER* 1.3 61.6 + - - +
87K SER 3.0 1.3 - - - -
88K LEU* 3.0 40.0 + - + +
89K GLN 4.1 0.9 + - - -
92K ARG* 4.7 4.0 + - - -
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Residues in contact with SER 86 (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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63K LEU* 3.5 23.4 - - - +
76K LYS* 5.6 4.0 + - - -
84K HIS* 2.9 31.9 + - - +
85K ASP* 1.3 76.0 - - - +
87K SER* 1.3 62.6 + - - +
88K LEU 3.2 0.2 - - - -
89K GLN* 3.2 21.4 + - - +
90K LEU* 4.1 0.7 + - - +
193K GLN 4.4 3.4 - - - -
194K THR 4.4 8.1 - - - -
195K GLY* 3.6 26.3 - - - +
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Residues in contact with SER 87 (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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76K LYS* 5.0 6.5 + - - +
83K ARG* 3.2 37.8 + - - +
84K HIS* 3.1 12.0 + - - +
85K ASP 3.0 0.4 - - - -
86K SER* 1.3 80.5 + - - +
88K LEU* 1.3 63.6 + - - +
89K GLN 3.4 0.5 + - - -
90K LEU* 3.5 18.0 + - - +
91K THR 4.4 0.2 + - - -
206L ASN* 4.3 10.9 + - - -
210L ASP* 2.7 29.8 + - - +
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Residues in contact with LEU 88 (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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83K ARG* 4.9 17.0 - - - +
84K HIS 5.3 0.2 - - - +
85K ASP* 3.0 32.2 + - + +
87K SER* 1.3 81.2 - - - +
89K GLN* 1.3 64.6 + - - +
90K LEU 3.4 0.5 + - - -
91K THR* 3.4 19.4 + - - +
92K ARG* 3.5 34.6 + - - +
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Residues in contact with GLN 89 (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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85K ASP 4.1 0.2 + - - -
86K SER* 3.2 15.9 + - - +
88K LEU* 1.3 77.4 - - - +
90K LEU* 1.3 60.4 + - - +
92K ARG* 3.1 28.3 + - - +
93K GLN* 2.8 28.1 + - - +
96K TRP* 3.9 6.7 - - - -
194K THR 3.4 22.9 - - - +
195K GLY 3.6 14.8 - - - +
196K CYS* 3.7 16.0 - - - -
273K VAL* 3.7 17.3 - - - +
277K ASN* 3.1 34.2 + - - +
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Residues in contact with LEU 90 (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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86K SER 4.1 0.4 + - - -
87K SER* 3.5 11.5 + - - +
88K LEU 3.3 0.8 - - - -
89K GLN* 1.3 77.9 - - - +
91K THR* 1.3 62.3 + - - +
93K GLN* 3.1 6.6 + - - +
94K LEU* 2.9 35.9 + - + +
195K GLY 3.8 11.6 + - - +
197K PHE* 3.7 31.4 - - + -
197L PHE* 3.9 17.7 - - + -
199L GLN* 3.7 42.4 - - + +
200L LEU* 4.3 15.3 - - + -
206L ASN* 3.8 13.7 - - - +
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Residues in contact with THR 91 (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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87K SER 4.5 0.7 + - - -
88K LEU* 3.6 14.4 + - - +
89K GLN 3.3 0.4 - - - -
90K LEU* 1.3 78.7 - - - +
92K ARG* 1.3 64.1 + - - +
94K LEU* 3.3 12.7 + - + +
95K ALA* 3.2 20.8 + - - +
206L ASN* 3.4 27.6 + - - +
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Residues in contact with ARG 92 (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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85K ASP 4.7 3.8 + - - -
88K LEU* 3.5 36.7 + - - +
89K GLN* 3.1 34.5 + - - +
91K THR* 1.3 81.4 - - - +
93K GLN* 1.3 61.4 + - - +
95K ALA* 3.1 17.3 + - - +
96K TRP* 3.2 18.0 + - - -
277K ASN* 3.6 29.5 - - + +
279K GLU* 3.9 18.9 + - - -
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Residues in contact with GLN 93 (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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89K GLN* 2.8 19.0 + - - +
90K LEU* 3.1 8.8 + - - +
92K ARG* 1.3 73.1 - - - +
94K LEU* 1.3 62.9 + - - +
96K TRP* 3.2 52.0 + - + +
195K GLY 4.4 1.0 - - - +
196K CYS* 3.1 13.8 - - - -
197K PHE* 2.8 78.0 + - + -
200K LEU 4.4 4.0 + - - -
213K LEU* 3.8 14.1 - - - +
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Residues in contact with LEU 94 (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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90K LEU* 2.9 28.9 + - + +
91K THR* 3.6 11.9 - - + +
92K ARG 3.2 0.4 - - - -
93K GLN* 1.3 77.5 - - - +
95K ALA* 1.3 59.1 + - - +
96K TRP 3.3 4.2 + - - +
197K PHE* 3.8 27.8 - - + -
94L LEU* 3.5 31.6 - - + -
197L PHE* 5.0 2.5 - - + -
200L LEU* 3.9 36.1 - - + -
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Residues in contact with ALA 95 (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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91K THR* 3.2 11.8 + - + +
92K ARG* 3.1 13.2 + - - +
93K GLN 3.1 0.8 - - - -
94K LEU* 1.3 78.1 - - - +
96K TRP* 1.3 64.5 + - - +
97K THR* 3.1 12.8 + - - +
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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