Contacts of the strand formed by residues 497 - 509 (chain C) in PDB entry 1NYE
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 SER 497 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495C PRO 3.2 1.8 - - - -
496C THR* 1.3 87.2 + - - +
498C ILE* 1.3 67.2 + - - +
499C ASP* 3.5 12.1 + - - -
523C GLU 4.7 1.1 - - - -
524C VAL 3.6 0.3 - - - -
525C ALA* 2.8 42.8 + - - +
630D HIS* 3.4 19.5 - - - -
631D TRP 3.4 9.2 - - - -
632D GLU* 4.6 1.6 - - - -
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Residues in contact with ILE 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C SER* 3.7 24.5 - - - +
484C LEU* 3.5 34.5 - - + -
485C SER* 4.1 4.3 - - - +
495C PRO* 3.9 27.6 - - + -
497C SER* 1.3 81.8 + - - +
499C ASP* 1.3 62.7 + - - +
500C THR* 3.5 22.9 - - + -
522C SER* 4.2 4.9 - - - +
523C GLU 3.9 3.8 - - - -
524C VAL* 3.8 13.9 - - + -
629D ALA 3.7 0.7 - - - +
630D HIS* 3.3 7.2 + - - -
631D TRP* 2.8 41.4 + - + +
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Residues in contact with ASP 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C SER* 3.5 17.7 + - - -
498C ILE* 1.3 71.3 - - - +
500C THR* 1.3 60.5 + - - +
521C LYS* 4.1 0.3 + - - +
522C SER* 3.3 1.2 + - - -
523C GLU* 2.8 52.6 + - + +
562C LYS* 5.9 0.9 + - - -
628D GLN* 4.4 11.6 - - - +
629D ALA 3.8 3.4 - - - -
630D HIS* 2.9 30.5 + - - +
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Residues in contact with THR 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477C ALA* 3.5 22.7 + - - +
480C PHE* 4.1 15.2 - - + -
481C SER* 3.2 25.0 + - - +
498C ILE* 3.5 10.3 - - + -
499C ASP* 1.3 74.4 - - - +
501C THR* 1.3 63.9 + - - +
520C LEU* 5.1 2.5 - - - +
521C LYS 3.2 9.2 - - - -
522C SER* 2.8 27.8 - - - +
628D GLN* 3.2 8.4 + - - +
629D ALA 3.0 28.0 + - - +
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Residues in contact with THR 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C ALA* 4.5 0.4 - - - -
500C THR* 1.3 75.1 + - - +
502C ALA* 1.3 73.0 + - - +
503C ASP* 4.1 5.8 - - + +
519C ALA 4.8 1.1 - - - +
520C LEU* 3.5 12.3 - - - +
521C LYS* 2.8 52.6 + - + +
626D LYS* 4.3 21.8 - - + +
627D GLY 3.5 7.4 + - - +
628D GLN* 3.2 22.2 + - - +
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Residues in contact with ALA 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C GLY* 2.9 39.5 - - - +
476C HIS* 4.7 0.9 - - + -
477C ALA* 4.0 4.3 - - + +
501C THR* 1.3 79.3 - - - +
503C ASP* 1.3 58.8 + - - +
504C VAL* 3.7 1.4 + - - -
518C ILE* 4.5 5.8 - - + -
519C ALA 3.7 4.7 - - - -
520C LEU* 4.0 15.5 - - + -
625D LYS 3.6 1.4 - - - +
626D LYS* 3.1 5.5 - - - -
627D GLY 2.8 34.1 + - - +
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Residues in contact with ASP 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C THR* 4.1 3.1 - - + +
502C ALA* 1.3 70.5 - - - +
504C VAL* 1.3 67.1 + - - +
505C SER* 3.9 2.7 + - - -
517C LYS 3.8 0.9 - - - +
518C ILE* 3.3 2.1 - - - -
519C ALA* 2.9 50.1 + - + +
624D HIS* 2.8 37.6 + - - +
625D LYS 3.5 4.2 - - - +
626D LYS* 3.3 34.9 + - + -
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Residues in contact with VAL 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C GLU* 3.5 45.5 - - + +
472C ILE* 4.7 3.6 - - + -
473C GLY* 3.6 23.6 - - - +
502C ALA 4.4 0.7 - - - +
503C ASP* 1.3 75.0 - - - +
505C SER* 1.3 63.5 + - - +
506C LEU 3.9 1.0 + - - -
515C ILE* 3.4 29.6 - - + -
517C LYS 3.7 4.5 - - - +
518C ILE* 4.1 19.1 - - + +
623D ILE 3.5 1.2 - - - +
624D HIS* 3.5 5.5 - - - -
625D LYS* 2.8 37.4 + - - +
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Residues in contact with SER 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503C ASP* 4.0 3.6 + - - -
504C VAL* 1.3 73.6 - - - +
506C LEU* 1.3 59.7 + - - +
507C ASP 3.8 0.7 - - - -
515C ILE* 3.2 6.7 - - - +
516C THR* 2.9 41.1 + - - -
517C LYS* 2.7 32.5 + - - +
622D THR* 3.9 13.2 - - - -
623D ILE 3.4 5.4 - - - -
624D HIS* 3.5 21.2 + - - -
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Residues in contact with LEU 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459C ARG* 5.0 3.6 - - - +
460C PHE* 3.9 18.4 - - + -
469C GLU* 3.7 30.3 - - + +
504C VAL 3.9 1.2 + - - +
505C SER* 1.3 71.6 - - - +
507C ASP* 1.3 58.9 + - - +
508C LYS* 4.3 0.5 + - - +
513C PHE* 3.2 41.3 - - + -
514C ALA 3.7 17.3 - - - +
515C ILE* 3.5 25.8 - - + +
622D THR* 4.0 0.6 - - - -
623D ILE* 3.0 47.2 + - + +
746D PRO* 4.1 11.9 - - + -
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Residues in contact with ASP 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C SER 3.8 0.2 - - - -
506C LEU* 1.3 73.9 - - - +
508C LYS* 1.3 90.5 + - - +
509C VAL* 3.0 15.5 + - + +
513C PHE* 3.3 8.0 - - - -
514C ALA 2.9 28.6 + - - +
516C THR* 3.8 28.0 + - + +
622D THR* 3.0 32.6 + - - +
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Residues in contact with LYS 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B LYS* 2.8 54.7 + - - +
261B GLU* 5.6 2.2 + - - -
506C LEU 5.3 0.2 - - - +
507C ASP* 1.3 93.9 + - - +
509C VAL* 1.3 62.0 + - - +
510C ASP 4.2 3.4 + - - +
512C GLY 3.7 3.6 - - - +
513C PHE* 3.3 31.0 - - + -
620D HIS* 2.9 39.3 - - + +
621D MET* 4.2 2.0 - - - +
622D THR* 3.8 11.1 - - - +
623D ILE* 6.5 0.7 - - + -
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Residues in contact with VAL 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C ASP* 3.0 18.1 + - + +
508C LYS* 1.3 75.6 - - - +
510C ASP* 1.3 89.1 + - - +
512C GLY 2.5 28.4 + - - +
513C PHE 5.0 0.2 - - - -
514C ALA* 4.4 13.5 - - + -
516C THR* 4.0 23.8 - - + -
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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