Contacts of the helix formed by residues 251 - 260 (chain A) in PDB entry 3ANX
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 GLY 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A SER 3.5 1.2 + - - -
250A GLU* 1.3 75.2 - - - +
252A VAL* 1.3 51.5 + - - +
253A ILE 3.9 0.7 - - - -
254A GLU* 3.6 14.1 - - - +
255A ALA* 2.8 31.5 + - - +
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Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A SER* 2.8 44.2 + - - +
250A GLU 3.1 12.8 - - - +
251A GLY* 1.3 71.4 - - - +
253A ILE* 1.3 71.0 + - + +
254A GLU 3.2 0.4 - - - -
255A ALA* 3.2 9.7 - - + +
256A ARG* 2.9 51.7 + - - +
273A GLU* 5.8 0.2 + - - -
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Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 4.1 33.0 - - + +
74A THR* 4.4 7.0 - - - +
248A PHE* 3.9 31.2 - - + -
249A SER 4.6 1.0 + - - +
252A VAL* 1.3 79.6 - - + +
254A GLU* 1.3 52.5 + - - +
256A ARG* 3.3 10.1 + - - +
257A ILE* 2.7 56.4 + - + +
269A ALA* 4.1 10.3 - - + -
272A LEU* 3.9 24.2 - - + -
273A GLU* 3.1 28.7 + - + +
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Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A GLY* 3.6 15.4 + - - +
252A VAL 4.1 0.6 - - - +
253A ILE* 1.3 75.4 - - - +
255A ALA* 1.4 70.4 + - - +
257A ILE* 3.0 21.9 + - - +
258A ARG* 2.9 60.9 + - - +
268A THR* 5.6 0.3 - - - -
269A ALA* 3.1 32.7 + - + +
270A PRO* 4.6 2.9 - - - +
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A GLY 2.8 21.0 + - - +
252A VAL* 3.0 17.0 + - + +
254A GLU* 1.4 74.6 - - - +
256A ARG* 1.3 58.1 + - + +
258A ARG* 3.0 19.3 + - - +
259A GLU* 3.1 28.9 + - + +
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Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 2.8 46.1 + - + -
74A THR* 3.8 15.6 + - - +
75A HIS 4.3 0.2 - - - -
76A PRO* 3.3 36.7 + - - +
252A VAL* 2.9 39.6 + - - +
253A ILE* 3.6 12.7 - - - +
255A ALA* 1.3 75.0 - - + +
257A ILE* 1.3 71.4 + - - +
259A GLU* 4.1 17.7 - - - +
260A ARG* 3.0 45.4 + - - +
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Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 3.6 31.6 - - + -
253A ILE* 2.7 36.0 + - + +
254A GLU* 3.0 15.0 + - - +
256A ARG* 1.3 77.2 - - - +
258A ARG* 1.4 56.6 + - - +
260A ARG* 3.8 0.7 - - - +
261A ASN* 3.1 18.4 + - - -
262A LEU* 3.2 35.9 + - + +
264A LEU* 4.2 16.8 - - + -
267A LEU* 6.2 0.2 - - + -
268A THR* 4.5 2.0 - - - -
269A ALA* 4.0 24.9 - - + +
272A LEU* 5.2 0.7 - - + -
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Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A GLU* 2.9 49.1 + - - +
255A ALA* 3.0 8.2 + - - +
257A ILE* 1.4 71.7 - - - +
259A GLU* 1.4 61.3 + - + +
260A ARG 2.9 1.3 - - - -
261A ASN* 2.6 35.3 + - - +
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PRO* 5.2 1.6 - - - +
255A ALA* 3.1 23.6 - - + +
256A ARG* 4.1 21.9 + - - +
258A ARG* 1.4 79.3 - - + +
260A ARG* 1.3 63.0 + - + +
261A ASN* 3.2 9.0 + - - -
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Residues in contact with ARG 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A MET 2.8 26.0 + - - -
73A LEU* 4.0 8.9 + - - +
75A HIS 3.0 20.4 + - - -
76A PRO 3.3 14.7 + - - -
78A PRO* 3.4 16.6 - - - +
97A LYS 4.4 3.8 - - - +
98A HIS* 3.1 35.2 + - - -
99A PRO* 3.3 41.8 - - + +
100A THR* 4.3 12.6 - - + +
256A ARG* 3.0 45.8 + - - +
257A ILE 4.1 1.8 - - - +
258A ARG 2.8 2.8 + - - -
259A GLU* 1.3 78.0 - - + +
261A ASN* 1.3 70.8 + - - +
262A LEU* 4.4 10.1 - - + -
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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