Contacts of the strand formed by residues 551 - 565 (chain A) in PDB entry 6T2C
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 THR 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A GLU* 6.0 1.3 - - + -
545A ILE 3.3 3.8 - - - +
546A ARG* 3.2 42.3 - - + +
547A THR 4.8 2.1 + - - -
550A SER* 1.3 83.4 + - - +
552A ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 552 (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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544A GLU* 3.4 6.2 - - - +
545A ILE* 2.9 47.2 + - + +
547A THR* 6.0 2.5 - - + -
550A SER* 3.4 25.8 - - - +
551A THR* 1.3 75.6 - - - +
553A MET* 1.3 69.4 + - - +
554A LYS* 3.7 29.6 - - + +
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Residues in contact with MET 553 (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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542A ASP* 3.8 34.5 - - + +
543A MET 3.3 11.4 - - - +
544A GLU* 2.6 49.1 - - + +
552A ILE* 1.3 80.0 - - - +
554A LYS* 1.3 66.7 + - - +
555A PRO* 4.6 1.7 - - - +
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Residues in contact with LYS 554 (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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522A LEU* 3.8 25.3 - - + +
542A ASP* 3.4 5.4 - - - -
543A MET* 2.9 35.6 + - + +
545A ILE* 3.4 34.0 - - + +
552A ILE* 3.7 22.4 - - + +
553A MET* 1.3 80.1 - - - +
555A PRO* 1.3 70.6 - - + +
556A VAL* 4.3 0.2 - - - +
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Residues in contact with PRO 555 (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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522A LEU* 3.5 14.2 - - - +
539A GLU* 3.3 25.6 - - + +
541A GLY 3.3 10.1 - - - +
542A ASP* 4.3 8.3 - - - +
553A MET 4.6 1.6 - - - +
554A LYS* 1.3 87.1 - - + +
556A VAL* 1.3 60.2 + - - +
557A TYR* 3.3 39.4 - - + +
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Residues in contact with VAL 556 (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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288A MET* 4.2 19.1 - - + -
314A PHE* 4.3 15.3 - - + -
520A PHE* 4.7 4.0 - - + -
521A SER 3.7 10.5 - - - +
522A LEU* 4.0 11.4 - - + -
539A GLU* 3.9 1.2 - - - +
540A ILE* 3.0 38.1 + - + +
541A GLY* 2.8 21.6 + - - +
543A MET* 3.7 40.2 - - + +
554A LYS 4.3 0.7 - - - +
555A PRO* 1.3 72.6 - - - +
557A TYR* 1.3 67.4 + - - +
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Residues in contact with TYR 557 (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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323A ILE* 3.6 23.8 - - + -
520A PHE* 3.5 4.0 - - - -
521A SER 2.9 32.3 + - - +
522A LEU 4.4 7.6 - - - -
523A THR 4.0 15.0 - - - -
524A ASP* 3.7 29.1 + - + +
525A PRO* 4.7 0.4 - - + -
526A ARG* 3.2 21.9 + - - -
537A VAL* 4.1 11.2 - - + -
538A LEU 3.3 18.4 - - - +
539A GLU* 3.7 27.0 + - + +
540A ILE* 4.5 1.6 - - - +
555A PRO* 3.3 37.8 - - + +
556A VAL* 1.3 77.7 - - - +
558A LEU* 1.3 62.0 + - - +
559A TYR* 4.3 8.5 - - + -
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Residues in contact with LEU 558 (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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338A TRP* 3.6 39.5 - - + -
498A PHE* 6.4 0.4 - - + -
518A LEU* 3.8 11.9 - - + +
519A GLU 3.6 31.2 - - - +
520A PHE* 3.7 24.0 - - + -
536A CYS 3.9 0.9 - - - +
537A VAL* 3.5 3.0 - - - -
538A LEU* 3.0 45.7 + - + -
540A ILE* 3.8 19.3 - - + -
557A TYR* 1.3 76.3 - - - +
559A TYR* 1.3 64.1 + - - +
560A VAL* 3.7 14.9 + - + +
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Residues in contact with TYR 559 (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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283A LEU* 3.8 15.3 - - + -
286A ASP* 5.8 0.2 - - + -
517A SER* 3.1 7.4 + - - +
518A LEU* 3.2 0.5 - - - -
519A GLU* 2.9 38.0 + - + +
521A SER* 3.5 35.2 - - - -
523A THR* 2.4 27.3 + - - -
525A PRO* 3.3 15.2 - - + +
532A TRP* 3.6 50.0 - + - -
535A TYR* 4.1 16.7 - + + -
536A CYS 4.4 2.0 - - - -
537A VAL* 3.6 35.4 - - + +
557A TYR* 4.3 5.2 - - + -
558A LEU* 1.3 74.3 - - - +
560A VAL* 1.3 60.4 + - - +
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Residues in contact with VAL 560 (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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334A TYR* 3.6 37.3 - - + +
337A ILE* 5.3 1.1 - - + -
516A ILE* 4.0 10.1 - - + -
517A SER 3.3 2.5 - - - -
518A LEU* 3.7 33.9 - - + -
535A TYR* 3.6 1.0 - - - -
536A CYS* 2.9 46.2 + - - +
538A LEU* 4.0 20.0 - - + -
558A LEU* 4.0 12.1 - - + +
559A TYR* 1.3 75.5 - - - +
561A ARG* 1.3 65.6 + - - +
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Residues in contact with ARG 561 (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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278A GLN 4.2 17.0 + - - -
279A ARG* 4.4 6.9 - - - +
280A SER 4.4 8.0 + - - -
334A TYR* 4.5 5.6 - - - -
516A ILE* 3.3 7.4 - - - +
517A SER* 2.9 48.1 + - - +
534A LYS* 3.6 34.7 + - - +
535A TYR* 3.6 35.7 + - + -
559A TYR 4.2 0.2 - - - -
560A VAL* 1.3 78.0 - - - +
562A THR* 1.3 70.5 + - - +
563A ASN* 3.1 33.0 + - + +
2V G 3.0 13.9 + - - -
3V U 2.6 31.1 + - - -
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Residues in contact with THR 562 (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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334A TYR* 2.5 32.4 + - - -
364A GLY* 3.2 29.3 + - - +
365A LEU* 5.0 2.2 - - - -
514A ASN* 5.0 4.5 - - + -
515A PHE 3.5 8.5 - - - +
516A ILE* 4.5 2.2 - - - +
534A LYS 5.2 1.2 + - - -
561A ARG* 1.3 76.8 + - - +
563A ASN* 1.3 57.7 + - - +
1V A 3.9 27.8 + - + +
2V G 2.5 46.2 + - - +
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Residues in contact with ASN 563 (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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279A ARG 5.4 0.6 + - - -
280A SER 4.0 12.3 + - - -
281A LYS* 2.7 41.1 + - - +
514A ASN* 3.5 6.8 - - - +
515A PHE* 2.9 53.5 + - + +
517A SER* 5.4 0.9 + - - +
561A ARG* 3.1 46.0 + - + +
562A THR* 1.3 75.9 - - - +
564A GLY* 1.3 69.9 + - - +
2V G 3.6 7.6 + - - -
3V U 3.9 6.4 - - - +
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Residues in contact with GLY 564 (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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281A LYS* 3.3 10.7 + - - -
512A VAL* 4.0 10.3 - - - -
513A VAL 3.4 11.2 - - - -
514A ASN* 4.2 3.6 - - - -
515A PHE* 3.9 4.0 - - - -
563A ASN* 1.3 90.4 + - - +
565A THR* 1.3 62.8 + - - -
569A LYS* 5.7 0.3 - - - +
2V G 3.9 3.8 + - - -
3V U 3.3 23.5 + - - -
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Residues in contact with THR 565 (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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281A LYS* 4.9 7.9 - - - +
461A ASN* 5.4 2.1 + - - -
464A LEU* 4.1 7.6 - - + -
512A VAL* 3.1 8.4 - - - +
513A VAL* 2.8 49.1 + - + +
515A PHE* 4.0 18.6 - - + -
564A GLY* 1.3 75.6 - - - -
566A SER* 1.3 67.6 + - - +
569A LYS* 3.6 23.0 - - - +
570A MET* 3.8 26.6 + - + +
3V U 4.4 4.0 - - - -
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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