Contacts of the strand formed by residues 3573 - 3580 (chain A) in PDB entry 2RT5
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 TYR3573 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3528A SER* 2.8 27.7 + - - -
3529A GLY* 3.3 16.4 - - - -
3530A ASN 3.0 19.2 + - - -
3533A LEU* 3.3 7.6 - - - +
3566A ARG* 3.5 28.0 - - + +
3567A MET* 3.1 47.1 + - + +
3569A VAL 4.0 4.9 - - - -
3570A GLU* 4.0 2.9 - - + -
3571A THR 3.8 2.9 + - - -
3572A ASP* 1.3 79.1 - - - +
3574A CYS* 1.3 62.3 + - - +
3575A LEU* 3.4 38.2 - - + +
3642A LEU* 3.8 3.1 - - - +
3660A VAL* 3.4 26.7 - - + -
3661A ILE 3.0 11.9 - - - +
3662A ALA* 4.5 5.2 - - + -
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Residues in contact with CYS3574 (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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3526A PHE* 3.6 21.5 - - - -
3528A SER 3.7 2.7 - - - -
3530A ASN 3.0 28.0 - - - +
3533A LEU* 3.6 13.9 - - + -
3534A ALA* 4.0 11.9 - - - -
3573A TYR* 1.3 77.5 - - - +
3575A LEU* 1.3 61.2 + - - +
3576A LEU* 3.6 20.9 - - - -
3659A ILE 3.6 1.6 - - - +
3660A VAL* 3.3 5.2 - - - -
3661A ILE* 2.7 47.1 + - + +
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Residues in contact with LEU3575 (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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3526A PHE* 4.0 0.2 - - - -
3527A VAL* 2.8 53.1 + - + -
3528A SER* 2.7 23.9 + - - +
3567A MET* 3.7 11.2 - - + -
3573A TYR* 3.4 28.5 - - + +
3574A CYS* 1.3 73.8 - - - +
3576A LEU* 1.3 66.4 + - - +
3639A LEU* 4.3 7.6 - - + -
3642A LEU* 3.3 28.5 - - + -
3658A MET* 4.1 18.8 - - + -
3659A ILE 3.8 0.2 - - - -
3660A VAL* 3.7 20.9 - - + -
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Residues in contact with LEU3576 (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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3508A VAL* 3.6 21.1 - - + -
3524A LEU* 3.3 29.2 - - + -
3525A HIS 3.4 2.2 - - - +
3526A PHE* 4.0 13.5 - - + -
3527A VAL* 3.5 6.0 - - - +
3534A ALA* 3.8 1.1 - - + -
3538A LEU* 3.7 21.3 - - + -
3574A CYS* 3.6 17.5 - - - -
3575A LEU* 1.3 83.5 - - - +
3577A LEU* 1.3 60.9 + - - +
3578A ALA 4.0 0.2 - - - -
3658A MET* 3.7 8.5 - - - +
3659A ILE* 2.7 40.0 + - + +
3661A ILE* 3.3 32.8 - - + -
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Residues in contact with LEU3577 (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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3523A GLN 3.2 4.2 - - - +
3524A LEU* 4.1 2.2 - - - -
3525A HIS* 2.7 42.7 + - + +
3527A VAL* 3.5 11.2 - - + -
3576A LEU* 1.3 76.2 - - - +
3578A ALA* 1.3 60.0 + - - +
3579A LEU* 3.6 26.6 + - + -
3639A LEU* 3.5 44.6 - - + -
3646A LEU* 3.7 21.1 - - + -
3650A ILE* 3.6 11.2 - - + -
3656A HIS* 3.5 26.5 - - + +
3657A LEU 3.9 3.8 - - - +
3658A MET* 4.7 1.6 - - - -
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Residues in contact with ALA3578 (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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3513A LEU* 4.6 1.1 - - + -
3522A VAL* 4.1 20.0 - - + -
3523A GLN 3.5 4.7 - - - -
3524A LEU* 3.9 10.3 - - + +
3576A LEU 4.0 1.4 - - - -
3577A LEU* 1.3 71.6 - - - +
3579A LEU* 1.3 60.5 + - - +
3580A PRO* 4.5 0.3 - - - +
3595A LEU* 5.0 1.7 - - - +
3656A HIS* 3.2 8.3 - - - +
3657A LEU* 3.0 38.3 + - + +
3659A ILE* 3.3 30.9 - - + +
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Residues in contact with LEU3579 (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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3496A VAL* 4.6 13.5 - - + -
3501A LEU* 6.4 0.9 - - + -
3522A VAL* 3.0 4.9 - - - -
3523A GLN* 2.7 49.9 + - + +
3525A HIS* 3.9 23.6 - - + +
3577A LEU* 3.6 16.2 - - + -
3578A ALA* 1.3 74.3 - - - +
3580A PRO* 1.3 68.6 - - + +
3581A CYS 3.1 0.2 + - - -
3646A LEU* 5.1 1.6 - - + -
3650A ILE* 3.7 17.5 - - + -
3653A ILE* 3.5 33.2 - - + -
3656A HIS* 3.2 29.2 - - + -
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Residues in contact with PRO3580 (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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3520A ALA* 6.3 0.2 - - + -
3521A ALA 3.2 9.4 - - - +
3522A VAL* 4.1 3.5 - - + -
3523A GLN* 4.3 5.2 + - - -
3578A ALA 4.5 0.2 - - - +
3579A LEU* 1.3 90.2 - - + +
3581A CYS* 1.3 62.1 + - - +
3582A GLY 3.5 3.6 + - - -
3588A VAL* 4.0 12.0 - - + +
3591A GLN* 3.9 11.4 - - + +
3592A THR* 3.4 44.0 - - - +
3595A LEU* 3.9 18.2 - - + -
3653A ILE* 4.0 15.5 - - + -
3655A PRO 4.0 11.2 - - - +
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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