Contacts of the helix formed by residues 149 - 155 (chain K) in PDB entry 5ANC
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 149 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147K LYS* 3.7 3.5 - - + +
148K ILE* 1.3 80.7 - - - +
150K ARG* 1.3 58.9 + - - +
151K LEU 3.3 0.7 - - - -
152K ILE* 3.7 17.4 - - + +
153K VAL* 2.9 34.2 + - + +
236K SER* 3.2 17.3 + - - +
238K ILE* 3.6 22.7 - - + +
241K TRP* 3.0 40.0 + - - -
243K PHE* 3.6 13.5 - - - -
298K LEU* 5.4 2.1 - - - +
301K ILE* 4.5 10.4 - - - +
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Residues in contact with ARG 150 (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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30K HIS* 5.1 3.8 + - - -
64K GLN* 3.5 24.9 + - - +
65K ILE* 5.2 9.2 + - - +
119K ALA 5.7 1.6 + - - -
120K VAL* 5.4 12.1 - - - +
146K ASN* 3.7 22.8 - - - +
147K LYS* 2.8 59.5 + - - +
149K ASP* 1.3 77.6 - - - +
151K LEU* 1.3 68.0 + - + +
154K GLU* 3.2 26.6 + - + +
155K LEU* 3.1 49.1 + - + +
165K HIS* 4.0 16.3 - - - -
238K ILE* 6.1 0.2 - - - -
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Residues in contact with LEU 151 (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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147K LYS 5.0 3.1 - - - +
148K ILE* 3.2 21.4 + - + +
150K ARG* 1.3 82.4 - - - +
152K ILE* 1.3 59.5 + - + +
155K LEU* 4.2 20.4 - - + -
156K LYS 4.4 0.9 - - - -
157K PHE* 2.8 57.6 + - + +
158K THR 5.5 1.8 - - - +
161K GLU* 4.0 6.7 - - + +
162K ALA* 3.8 34.8 - - + +
165K HIS* 3.8 32.5 - - + +
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Residues in contact with ILE 152 (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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148K ILE* 3.7 14.4 - - + +
149K ASP* 3.6 18.5 + - - +
150K ARG 3.2 0.4 - - - -
151K LEU* 1.3 85.4 - - + +
153K VAL* 1.3 65.8 + - + +
156K LYS* 3.6 26.4 - - - +
157K PHE 4.1 13.0 + - - +
158K THR 4.8 0.2 - - - -
159K PRO* 4.1 31.4 - - + -
162K ALA* 6.5 0.2 - - + -
298K LEU* 5.0 12.8 - - + +
301K ILE* 4.5 12.3 - - + -
302K TRP* 4.1 30.8 - - + +
305K TYR* 3.9 17.4 - - + -
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Residues in contact with VAL 153 (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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149K ASP* 2.9 15.2 + - + +
152K ILE* 1.3 85.3 - - + +
154K GLU* 1.3 70.1 + - + +
156K LYS* 3.9 7.0 + - - +
238K ILE* 3.4 32.1 - - + -
305K TYR* 3.2 52.0 + - + +
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Residues in contact with GLU 154 (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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96B HIS 5.2 6.1 - - - +
61K GLU* 5.4 2.8 - - - +
65K ILE* 3.6 31.7 - - - +
147K LYS* 4.8 9.7 + - - -
149K ASP 4.1 0.4 + - - -
150K ARG* 3.2 25.5 + - + +
153K VAL* 1.3 85.7 - - + +
155K LEU* 1.3 69.8 + - + +
156K LYS* 4.8 1.2 - - - +
3359N U 3.8 23.4 + - - +
3360N A 4.6 0.9 + - - -
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Residues in contact with LEU 155 (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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95B ALA* 4.7 18.0 - - - +
96B HIS* 5.6 12.1 - - + -
98B PRO* 5.6 4.2 - - - +
150K ARG* 3.1 27.3 + - + +
151K LEU* 4.2 18.2 - - + -
154K GLU* 1.3 80.7 - - + +
156K LYS* 1.3 73.0 + - - +
157K PHE* 3.7 42.9 - - + -
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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