Contacts of the strand formed by residues 3518 - 3529 (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 ASP3518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3515A LEU* 2.9 30.5 + - + +
3516A LYS* 4.0 9.9 - - - +
3517A ASN* 1.3 88.9 + - - +
3519A THR* 1.3 61.2 + - - +
3594A SER* 6.4 0.4 - - - -
3598A ALA* 3.4 31.0 - - + +
3599A PHE* 3.3 9.2 - - - -
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Residues in contact with THR3519 (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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3512A LEU* 4.0 20.7 - - + +
3513A LEU 3.1 5.6 - - - +
3514A ALA* 3.7 21.8 - - + -
3517A ASN 3.8 8.8 + - - +
3518A ASP* 1.3 78.7 - - - +
3520A ALA* 1.3 63.7 + - - +
3521A ALA 4.3 0.2 - - - -
3546A PRO* 4.8 7.4 - - + -
3591A GLN* 4.4 3.0 + - - -
3594A SER* 3.9 17.8 - - - -
3599A PHE* 4.3 1.3 - - - -
2524B SEP 5.1 3.8 - - - +
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Residues in contact with ALA3520 (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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3512A LEU* 4.1 1.6 - - - -
3513A LEU* 2.8 34.2 + - + -
3519A THR* 1.3 75.6 - - - +
3521A ALA* 1.3 64.2 + - - +
3522A VAL* 3.2 8.9 + - + +
3580A PRO* 6.3 0.2 - - + -
3591A GLN* 3.6 8.3 - - - +
3595A LEU* 3.5 49.4 - - + +
3599A PHE* 4.1 8.0 - - + -
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Residues in contact with ALA3521 (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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3510A GLN* 5.2 0.9 - - - +
3511A GLY 3.1 12.6 - - - +
3512A LEU* 3.5 21.6 - - + +
3520A ALA* 1.3 69.3 - - - +
3522A VAL* 1.3 54.5 + - - +
3580A PRO* 3.2 8.1 - - - +
3581A CYS* 2.8 44.9 + - - +
3587A ASP* 6.0 0.2 - - - +
3591A GLN* 2.9 27.9 - - + +
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Residues in contact with VAL3522 (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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3509A TRP* 4.3 7.1 - - + -
3510A GLN* 3.7 0.5 - - - -
3511A GLY 2.8 33.4 + - - +
3512A LEU 4.5 2.0 - - - -
3513A LEU* 3.4 42.6 - - + +
3520A ALA* 3.5 12.8 - - + +
3521A ALA* 1.3 79.4 - - - +
3523A GLN* 1.3 59.2 + - - +
3524A LEU* 4.3 3.5 + - + -
3578A ALA* 4.1 17.3 - - + -
3579A LEU 3.0 19.7 - - - +
3580A PRO* 4.1 0.9 - - + -
3581A CYS* 3.3 5.6 - - - -
3595A LEU* 4.0 22.4 - - + -
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Residues in contact with GLN3523 (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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3498A MET* 4.6 10.3 - - - +
3507A ILE* 3.4 22.7 - - + +
3509A TRP 3.6 5.6 - - - +
3510A GLN* 3.8 16.0 - - + +
3522A VAL* 1.3 73.7 - - - +
3524A LEU* 1.3 61.9 + - - +
3525A HIS* 3.7 21.4 + - - +
3577A LEU 3.2 3.1 - - - +
3579A LEU* 2.7 42.1 + - + +
3580A PRO 4.3 4.8 + - - -
3581A CYS* 3.6 28.2 - - + +
3582A GLY 5.3 0.2 - - - +
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Residues in contact with LEU3524 (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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3507A ILE* 3.2 6.6 - - - +
3508A VAL* 2.8 41.1 + - + +
3509A TRP* 2.7 53.9 + - + +
3513A LEU* 5.4 0.2 - - + -
3522A VAL* 4.9 4.0 - - + -
3523A GLN* 1.3 73.1 - - - +
3525A HIS* 1.3 60.4 + - - +
3538A LEU* 4.1 13.2 - - + -
3547A LEU* 4.8 2.2 - - + -
3576A LEU* 3.3 34.8 - - + -
3577A LEU 3.3 2.9 - - - -
3578A ALA* 3.9 13.9 - - + +
3659A ILE* 3.4 31.2 - - + -
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Residues in contact with HIS3525 (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* 5.8 0.4 - - + +
3498A MET* 3.5 41.3 - - + +
3501A LEU* 3.5 27.6 - - + +
3502A LEU* 5.9 0.8 - - - +
3505A TYR 4.6 0.4 - - - +
3507A ILE* 3.4 27.5 + - + +
3523A GLN* 3.9 20.7 + - - +
3524A LEU* 1.3 73.6 - - - +
3526A PHE* 1.3 67.1 + - - +
3576A LEU* 3.4 4.5 - - - -
3577A LEU* 2.7 53.4 + - + +
3579A LEU* 3.9 28.2 - - + +
3646A LEU* 4.5 5.6 - - + -
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Residues in contact with PHE3526 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3504A LYS 4.6 4.5 - - - -
3505A TYR* 2.8 51.5 - + + +
3506A PRO* 2.8 28.4 + - + +
3508A VAL* 3.8 11.8 - - + +
3524A LEU 3.9 1.4 + - - -
3525A HIS* 1.3 74.6 - - - +
3527A VAL* 1.3 66.5 + - - +
3528A SER* 3.1 29.6 - - - -
3529A GLY 3.3 22.7 - - - -
3531A ASN* 3.5 42.0 - - + -
3574A CYS* 3.6 14.4 - - - -
3575A LEU 4.0 1.1 - - - -
3576A LEU* 4.0 8.3 - - + -
3646A LEU* 3.9 2.9 - - - +
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Residues in contact with VAL3527 (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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3505A TYR* 3.6 22.6 - - - +
3526A PHE* 1.3 81.2 - - - +
3528A SER* 1.3 59.9 + - - +
3575A LEU* 2.8 37.1 + - + +
3576A LEU 3.5 7.4 - - - +
3577A LEU* 3.4 41.1 - - + +
3639A LEU* 3.8 17.3 - - + -
3642A LEU* 4.2 10.1 - - + +
3643A ALA* 3.3 25.6 - - + -
3646A LEU* 3.6 5.4 - - + -
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Residues in contact with SER3528 (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* 3.1 19.2 - - - -
3527A VAL* 1.3 80.6 - - - +
3529A GLY* 1.3 60.2 + - - +
3570A GLU* 2.6 27.4 + - - +
3573A TYR* 2.8 25.4 + - - -
3575A LEU* 2.7 38.5 + - - -
3642A LEU* 3.3 18.5 - - - +
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Residues in contact with GLY3529 (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* 3.3 13.4 - - - -
3528A SER* 1.3 73.9 + - - +
3530A ASN* 1.3 60.5 + - - -
3531A ASN* 3.7 0.5 + - - -
3570A GLU* 2.8 41.9 + - - +
3571A THR 4.4 0.2 - - - -
3573A TYR* 3.3 18.8 - - - -
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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