Contacts of the strand formed by residues 297 - 302 (chain A) in PDB entry 4ND1
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 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PHE* 3.6 24.7 - - - -
158A ASN 3.3 9.6 - - - -
159A LYS* 4.5 1.3 - - - -
261A TYR* 3.6 6.8 - - - -
293A ILE* 3.3 6.1 - - - -
294A GLY 3.0 31.9 + - - -
295A LYS 3.4 1.8 - - - -
296A ASN* 1.3 72.5 - - - +
298A VAL* 1.3 61.9 + - - -
299A GLU* 3.2 7.3 + - - +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 4.6 1.3 - - + -
157A HIS 5.2 0.9 - - - +
158A ASN* 2.9 41.3 + - - +
160A VAL 5.1 1.8 - - - +
161A CYS* 4.1 30.5 - - + -
271A CYS* 4.6 3.1 - - - -
273A ALA* 4.1 17.7 - - + -
291A THR* 3.9 16.6 - - + -
292A ILE 3.6 3.8 - - - -
293A ILE* 4.5 11.4 - - + -
296A ASN 4.1 1.2 - - - +
297A GLY* 1.3 67.8 - - - -
299A GLU* 1.3 60.0 + - - +
301A ASP 3.9 18.8 - - - +
302A ILE* 4.7 5.6 - - + -
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Residues in contact with GLU 299 (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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266A LYS* 2.8 37.0 + - - +
292A ILE* 2.8 16.6 + - + +
293A ILE 4.6 0.2 - - - -
294A GLY* 3.7 10.5 - - - +
295A LYS 3.1 11.6 + - - -
296A ASN* 2.9 42.2 + - + +
297A GLY 3.3 15.3 - - - +
298A VAL* 1.3 74.3 - - - +
301A ASP* 1.3 65.1 + - + +
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Residues in contact with ASP 301 (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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278A HIS* 4.7 7.1 + - - -
291A THR* 3.3 8.0 - - - -
292A ILE* 2.9 42.9 + - + -
298A VAL* 3.5 4.0 - - - +
299A GLU* 1.3 81.7 - - + +
302A ILE* 1.3 91.6 + - - +
303A LEU* 5.5 4.0 - - - -
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Residues in contact with ILE 302 (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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273A ALA* 4.7 4.5 - - + -
274A PHE 3.8 24.0 - - - +
275A CYS* 3.8 17.7 - - + -
276A SER 5.1 0.2 - - - +
278A HIS* 3.6 37.4 + - + -
279A TYR* 4.0 10.1 - - + -
289A VAL* 4.0 30.3 - - + -
290A PRO 3.5 9.2 - - - +
291A THR* 4.3 7.2 - - + -
298A VAL* 4.7 5.8 - - + -
301A ASP* 1.3 95.9 + - - +
303A LEU* 1.3 78.0 + - - +
304A GLU 4.1 0.3 + - - -
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Residues in contact with LEU 303 (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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268A VAL* 4.1 34.8 - - + -
278A HIS* 5.2 0.2 - - - -
279A TYR* 2.7 31.9 + - - -
290A PRO* 2.9 26.8 + - + +
292A ILE* 4.1 23.8 - - + -
301A ASP* 5.5 4.0 - - - -
302A ILE* 1.3 80.8 - - - +
304A GLU* 1.3 56.3 + - - +
305A LEU* 3.9 2.5 - - + -
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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