Contacts of the strand formed by residues 306 - 312 (chain A) in PDB entry 4N25
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 PRO 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A LEU 3.6 4.7 - - - +
305A PRO* 1.3 88.8 - - + +
307A VAL* 1.3 61.6 + - - +
331A THR* 5.9 0.9 - - + -
332A ASN 5.8 0.2 - - - -
333A CYS* 3.5 30.1 - - - -
594A LEU* 3.8 24.0 - - + -
595A ASP* 3.5 26.2 - - - +
651A VAL* 3.6 22.9 - - + -
652A ARG 3.8 5.4 - - - +
653A ARG* 3.9 6.5 - - + +
654A LYS* 5.3 2.6 - - - -
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Residues in contact with VAL 307 (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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306A PRO* 1.3 79.0 - - - +
308A SER* 1.3 68.8 + - - +
332A ASN 4.9 0.3 - - - +
333A CYS* 3.5 8.5 - - - -
334A GLU* 3.2 25.2 + - - +
652A ARG* 2.8 42.3 + - - +
653A ARG 3.9 2.9 - - - -
654A LYS* 3.7 41.5 - - + +
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Residues in contact with SER 308 (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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307A VAL* 1.3 88.5 - - - +
309A VAL* 1.3 63.7 + - - +
310A PHE* 3.6 27.0 + - - -
333A CYS* 5.6 0.2 - - - -
334A GLU* 2.9 35.6 + - - +
336A LYS* 4.5 3.6 - - - -
651A VAL* 3.5 4.5 - - - +
652A ARG* 2.9 38.0 + - - +
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A SER* 1.3 74.8 - - - +
310A PHE* 1.3 63.2 + - - +
311A VAL* 4.0 20.2 - - + -
324A VAL* 5.0 2.0 - - + -
328A VAL* 3.9 25.1 - - + -
333A CYS* 4.2 12.8 - - + -
334A GLU 2.8 12.0 + - - +
335A LEU* 3.5 8.8 - - + +
336A LYS* 2.8 28.5 + - - +
592A ILE* 4.6 15.9 - - + -
594A LEU* 3.7 29.2 - - + -
649A THR* 5.0 3.1 - - - -
650A ASN 3.9 6.1 - - - +
651A VAL* 4.5 5.2 - - + +
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Residues in contact with PHE 310 (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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308A SER* 3.6 26.0 - - - -
309A VAL* 1.3 75.1 - - - +
311A VAL* 1.3 61.8 + - - +
336A LYS* 3.5 32.5 - - + +
338A CYS* 4.6 12.1 - - - -
349A ILE* 3.2 24.6 - - + +
355A PHE* 3.5 37.9 - + + -
390A PHE* 4.6 11.4 - + - -
649A THR* 3.2 4.7 - - - -
650A ASN 2.8 39.6 + - - +
652A ARG* 3.9 9.9 - - + -
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Residues in contact with VAL 311 (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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309A VAL* 4.0 9.2 - - + -
310A PHE* 1.3 80.9 - - - +
312A CYS* 1.3 65.4 + - - +
313A CYS* 4.6 5.4 - - - -
320A PHE* 3.3 32.3 - - + -
321A LEU* 4.7 9.6 - - + -
324A VAL* 3.9 24.9 - - + -
335A LEU* 4.2 6.5 - - + -
336A LYS 3.0 10.2 + - - +
337A VAL* 5.0 3.6 - - + -
338A CYS* 2.8 32.2 + - - +
349A ILE* 4.3 2.2 - - - -
648A GLY 3.3 3.4 - - - -
649A THR* 3.6 21.3 - - + -
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Residues in contact with CYS 312 (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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311A VAL* 1.3 76.8 - - - +
313A CYS* 1.3 66.2 + - - +
338A CYS* 3.0 15.0 - - + +
339A PHE 4.4 0.2 - - - +
340A GLN* 4.4 2.7 - - - +
346A ASP 3.3 23.3 - - - -
347A ARG 3.9 1.6 - - - -
348A TRP* 3.7 23.6 - - + +
349A ILE* 3.3 43.4 - - + +
647A CYS* 3.3 3.3 - - - +
648A GLY 2.9 35.7 + - - +
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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