Contacts of the strand formed by residues 414 - 419 (chain A) in PDB entry 3RT0
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 GLU 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A ASP* 5.8 0.9 - - - -
341A VAL 3.8 1.4 - - - +
342A SER* 3.6 0.5 - - - -
343A ASN* 2.9 34.8 + - + +
362A VAL* 5.6 6.2 - - - +
364A HIS* 2.8 30.0 + - + +
368A ARG* 2.9 29.6 + - - -
398A ARG* 4.0 13.0 + - - +
413A PRO* 1.3 77.6 - - - +
415A VAL* 1.3 64.5 + - - +
416A THR* 4.2 1.1 + - - -
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLN* 2.8 36.2 + - - +
286A TRP* 3.9 16.2 - - + +
287A ASP* 3.9 22.8 + - - +
290A PHE* 3.8 31.9 - - + -
291A THR* 5.8 0.2 - - - +
340A VAL* 3.8 22.7 - - + -
341A VAL 3.3 8.3 - - - +
342A SER* 4.1 5.2 - - - +
413A PRO* 5.0 3.8 - - + +
414A GLU* 1.3 80.4 - - - +
416A THR* 1.3 68.7 + - - +
417A PHE* 4.7 1.8 - - + +
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Residues in contact with THR 416 (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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339A ILE 3.8 1.2 - - - +
340A VAL* 3.4 7.3 - - - +
341A VAL* 2.8 37.8 + - - +
360A LEU* 2.8 50.7 + - + +
361A SER* 4.6 2.6 - - - -
414A GLU 4.2 1.3 + - - -
415A VAL* 1.3 75.4 + - - +
417A PHE* 1.3 69.2 + - - +
418A MET* 4.5 7.1 - - + +
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Residues in contact with PHE 417 (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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219A MET 3.7 17.9 - - - -
220A LEU* 3.5 18.2 - - + -
282A ARG* 3.6 22.7 - - + -
283A GLN* 4.2 27.2 - - + +
286A TRP* 3.6 23.8 - + + -
338A HIS* 3.1 42.2 - + - -
339A ILE 4.1 1.3 - - - -
340A VAL* 4.0 12.3 - - + +
415A VAL* 4.2 3.4 + - + -
416A THR* 1.3 76.5 - - - +
418A MET* 1.3 62.4 + - - +
419A PRO* 3.8 13.0 - - + +
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Residues in contact with MET 418 (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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338A HIS* 3.5 3.1 - - - -
339A ILE* 2.9 47.3 + - + +
351A LEU* 4.2 15.3 - - + -
353A ARG* 3.8 18.6 - - - +
358A MET* 5.7 3.6 - - - -
360A LEU* 3.9 33.9 - - + -
416A THR* 4.5 8.5 - - + +
417A PHE* 1.3 78.5 - - - +
419A PRO* 1.3 110.9 - - + +
420A ARG* 4.2 0.3 - - - -
362B VAL* 4.4 24.7 - - + -
368B ARG* 5.4 4.3 - - - +
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Residues in contact with PRO 419 (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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337A SER 3.6 2.0 - - - +
338A HIS* 3.5 26.4 - - + +
353A ARG* 2.8 21.5 + - - -
417A PHE* 3.8 15.0 - - + +
418A MET* 1.3 104.2 - - + +
420A ARG* 1.3 64.1 + - - +
368B ARG* 5.0 6.8 - - - +
370B ASP* 3.6 45.5 - - + +
414B GLU* 6.2 0.2 - - - +
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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