Contacts of the strand formed by residues 3507 - 3515 (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 ILE3507 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3498A MET* 4.3 9.0 - - + -
3502A LEU* 5.2 2.4 - - + +
3506A PRO* 1.3 80.0 - - - +
3508A VAL* 1.3 60.6 + - - +
3509A TRP 3.2 22.9 - - - +
3510A GLN* 4.9 4.7 - - + -
3523A GLN* 3.4 28.0 - - + +
3524A LEU 3.2 18.4 - - - +
3525A HIS* 3.4 34.1 - - + +
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Residues in contact with VAL3508 (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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3506A PRO* 3.9 2.2 - - + +
3507A ILE* 1.3 76.9 - - - +
3509A TRP* 1.3 66.7 + - - +
3524A LEU* 2.8 18.8 + - + +
3526A PHE* 3.8 33.0 - - + +
3531A ASN* 4.8 10.5 - - + +
3534A ALA* 3.8 13.9 - - + -
3535A HIS* 5.4 9.8 + - + +
3538A LEU* 3.7 19.4 - - + +
3576A LEU* 3.6 24.0 - - + -
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Residues in contact with TRP3509 (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 11.1 - - - +
3508A VAL* 1.3 84.7 - - - +
3510A GLN* 1.3 63.0 + - - +
3511A GLY* 3.6 22.4 - - - -
3512A LEU 3.5 28.7 - - - -
3522A VAL* 4.3 5.6 - - + -
3524A LEU* 2.7 60.0 + - + -
3538A LEU* 3.3 44.7 - - + +
3539A PRO* 2.8 24.2 + - + -
3540A LEU* 4.6 4.9 - - + +
3543A GLY 4.1 4.4 + - - -
3544A GLY* 3.4 22.2 - - - -
3545A PRO 3.4 27.1 - - - -
3547A LEU* 4.2 17.0 - - + -
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Residues in contact with GLN3510 (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* 4.9 4.7 - - + -
3509A TRP* 1.3 84.9 - - - +
3511A GLY* 1.3 63.3 + - - +
3521A ALA* 5.2 0.7 - - - +
3522A VAL 3.7 3.8 - - - -
3523A GLN* 3.8 23.8 - - + +
3543A GLY* 3.3 27.3 + - - +
3544A GLY* 4.2 0.3 - - - -
3581A CYS* 3.0 26.4 - - + +
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Residues in contact with GLY3511 (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* 3.6 13.8 - - - -
3510A GLN* 1.3 80.9 - - - +
3512A LEU* 1.3 69.8 + - - +
3521A ALA* 3.1 9.2 - - - +
3522A VAL 2.8 32.1 + - - +
3544A GLY 3.7 9.4 - - - -
3581A CYS* 3.8 2.3 - - - -
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Residues in contact with LEU3512 (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* 3.5 12.4 - - - -
3510A GLN* 6.1 0.2 - - - +
3511A GLY* 1.3 84.8 - - - +
3513A LEU* 1.3 61.9 + - - +
3519A THR* 4.0 22.9 - - + +
3520A ALA 3.3 5.6 - - - +
3521A ALA* 3.5 26.5 - - + +
3522A VAL* 4.1 0.9 - - - +
3544A GLY 4.0 8.2 + - - +
3546A PRO* 3.0 23.0 - - + +
3547A LEU 2.8 27.4 + - - -
3591A GLN* 5.3 2.0 - - - +
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Residues in contact with LEU3513 (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* 4.8 1.3 - - + -
3512A LEU* 1.3 76.9 - - - +
3514A ALA* 1.3 62.1 + - - +
3519A THR* 3.1 7.3 - - - -
3520A ALA* 2.8 33.0 + - + +
3522A VAL* 3.4 28.9 - - + -
3524A LEU* 5.4 0.7 - - + -
3546A PRO* 4.4 0.4 - - - -
3547A LEU* 3.4 39.5 - - + +
3578A ALA* 4.6 0.4 - - + -
3595A LEU* 4.9 0.9 - - + -
3599A PHE* 3.2 19.9 - - + -
3612A ILE* 4.3 5.8 - - + -
3628A ILE* 3.9 13.7 - - + -
3657A LEU* 3.4 32.8 - - + -
3659A ILE* 4.3 12.8 - - + -
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Residues in contact with ALA3514 (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* 1.3 77.7 - - - +
3515A LEU* 1.3 60.6 + - - +
3518A ASP 3.5 6.1 - - - +
3519A THR* 3.7 14.4 - - + -
3546A PRO* 3.7 23.3 - - + +
3547A LEU 2.7 10.7 + - - +
3548A ARG* 3.0 29.4 - - - +
3549A ILE 3.1 4.9 + - - -
3599A PHE* 3.8 2.0 - - - -
2523B ASP* 4.5 1.1 - - - +
2524B SEP 4.1 23.6 - - - +
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Residues in contact with LEU3515 (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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3514A ALA* 1.3 75.8 - - - +
3516A LYS* 1.3 90.3 + - + +
3517A ASN 2.8 9.4 + - - -
3518A ASP* 2.9 20.8 + - + +
3549A ILE* 3.7 23.6 - - + +
3598A ALA* 3.5 16.4 - - + +
3599A PHE* 3.4 47.7 - - + -
3602A TYR* 4.1 15.5 - - + -
3603A LEU* 5.0 1.6 - - + -
2521B LEU* 3.4 24.7 - - + -
2522B SEP 3.9 4.9 - - - +
2523B ASP* 4.5 2.9 - - - +
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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