Contacts of the strand formed by residues 554 - 569 (chain D) in PDB entry 2C11
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 554 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C LEU* 3.2 32.4 - - - +
551D VAL* 2.8 20.8 + - - +
553D TRP* 1.3 77.9 - - - +
555D PRO* 1.3 59.0 - - - +
556D GLU* 2.6 49.9 + - - +
557D HIS* 2.8 14.4 + - - +
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Residues in contact with PRO 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550D ALA* 4.1 19.6 - - + +
551D VAL 3.5 9.6 - - - +
552D PRO* 4.0 11.0 - - + +
553D TRP 3.9 0.9 - - - -
554D SER* 1.3 86.3 - - - +
556D GLU* 1.3 59.1 + - + +
557D HIS 3.3 4.7 - - - +
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Residues in contact with GLU 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C GLN* 4.1 6.3 + - - -
554D SER* 2.6 32.3 + - - +
555D PRO* 1.3 75.4 - - - +
557D HIS* 1.3 89.4 + - - +
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Residues in contact with HIS 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C LEU* 3.9 31.4 - - + +
219C GLN* 2.8 52.2 + - + +
550D ALA* 3.6 9.9 - - - +
551D VAL* 3.3 24.6 + - + -
554D SER* 2.8 13.5 + - - +
555D PRO 4.1 0.3 - - - +
556D GLU* 1.3 127.3 + - + +
558D GLN* 1.3 63.4 + - - +
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Residues in contact with GLN 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618C ASN* 5.5 6.2 - - - +
619C SER* 5.6 3.7 + - - -
620C SER* 4.7 11.8 + - - +
548D PRO* 3.4 29.3 - - - +
549D MET* 3.5 21.0 - - - +
550D ALA* 3.8 4.5 + - - +
551D VAL* 4.1 5.3 - - - +
557D HIS* 1.3 79.5 - - - +
559D LEU* 1.3 68.9 + - - +
560D GLN* 4.9 8.2 + - + +
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Residues in contact with LEU 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380C MET* 3.5 33.4 - - + +
381C THR* 3.8 20.0 - - + -
383C ARG* 5.6 0.2 - - - +
619C SER* 5.8 0.7 - - - -
1740C CL 4.0 10.8 - - + -
548D PRO* 3.5 3.6 - - - +
549D MET* 3.0 54.0 + - + +
550D ALA 4.3 2.0 - - - +
551D VAL* 4.0 24.4 - - + +
552D PRO* 4.1 1.3 - - + -
558D GLN* 1.3 76.8 - - - +
560D GLN* 1.3 63.7 + - - +
561D ARG* 3.2 40.4 - - + +
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Residues in contact with GLN 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C ARG* 2.9 21.5 + - - -
615C LEU* 3.9 4.0 - - + -
616C PRO* 3.9 23.5 - - + +
618C ASN* 3.7 13.9 - - - +
619C SER* 3.4 43.4 + - - +
1740C CL 3.1 13.0 - - + +
546D PHE* 3.4 22.7 - - + +
547D VAL 3.9 1.0 - - - -
548D PRO* 3.1 40.0 - - - +
558D GLN* 4.9 6.3 + - + +
559D LEU* 1.3 73.7 - - - +
561D ARG* 1.3 65.1 + - - +
562D LEU 3.3 0.9 + - - -
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Residues in contact with ARG 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C GLY 2.6 32.6 + - - +
375C ASN* 3.3 18.0 + - - +
380C MET* 3.0 37.9 - - - +
383C ARG* 4.8 1.6 - - - +
507C TYR* 3.3 37.3 + - + +
546D PHE* 3.5 2.1 - - - -
547D VAL* 2.8 46.3 + - + +
549D MET* 3.6 28.8 - - + +
552D PRO* 5.9 1.2 - - - +
559D LEU* 3.2 17.0 - - + +
560D GLN* 1.3 70.1 - - - +
562D LEU* 1.3 64.9 + - - +
563D GLN* 3.6 9.6 + - + +
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Residues in contact with LEU 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C ILE* 3.4 29.8 - - + +
372C TYR 3.5 23.6 - - - +
373C GLY* 3.6 9.7 - - - -
383C ARG* 4.6 1.2 - - - +
506C LYS 4.2 0.2 - - - +
507C TYR* 3.5 23.6 - - - -
519C VAL* 3.9 23.4 - - + +
520C HIS* 4.1 5.6 - - - -
521C THR* 4.4 7.4 - - + -
683C LEU* 5.5 0.2 - - + -
544D MET* 3.3 32.8 - - + -
545D VAL 3.6 11.2 - - - +
546D PHE* 3.5 20.0 - - + -
560D GLN 3.3 3.6 + - - +
561D ARG* 1.3 74.3 - - - +
563D GLN* 1.3 63.2 + - - +
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Residues in contact with GLN 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C LYS* 3.2 40.0 + - + +
507C TYR* 3.4 25.1 + - + -
519C VAL* 4.9 1.4 - - - +
544D MET* 3.4 6.4 - - - +
545D VAL* 2.9 41.3 + - + +
547D VAL* 3.1 37.3 - - + +
549D MET* 4.8 8.5 - - - +
561D ARG* 3.8 8.9 - - + +
562D LEU* 1.3 81.1 - - - +
564D VAL* 1.3 67.8 + - - +
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Residues in contact with VAL 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C GLY 3.8 15.6 - - - +
506C LYS* 2.7 34.0 + - - +
508C GLY 4.2 7.4 - - - +
519C VAL* 3.7 32.1 - - + -
685C ILE* 4.2 24.0 - - + -
542D GLU* 4.4 6.1 - - + -
543D ASP 3.3 13.7 - - - +
563D GLN* 1.3 80.8 - - - +
565D THR* 1.3 73.3 + - - +
566D ARG* 4.1 14.6 + - - +
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Residues in contact with THR 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541D ALA 3.6 1.7 - - - +
542D GLU* 3.1 4.2 - - - -
543D ASP* 2.8 49.5 + - - +
544D MET 3.6 9.1 + - - +
545D VAL* 3.2 34.1 - - + -
564D VAL* 1.3 74.0 - - - +
566D ARG* 1.3 59.4 + - - +
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Residues in contact with ARG 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C GLY* 3.0 40.2 + - - -
508C GLY 5.3 2.0 + - - +
509C ASN* 4.0 14.1 + - - -
685C ILE* 5.9 0.6 - - - +
540D TRP* 3.9 31.9 - - + -
541D ALA 3.6 3.1 - - - -
542D GLU* 3.0 37.7 + - + +
564D VAL* 4.1 9.4 + - + +
565D THR* 1.3 74.8 - - - +
567D LYS* 1.3 63.8 + - - +
588D TYR* 4.8 1.5 + - - -
599D HIS* 5.6 3.6 + - - -
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Residues in contact with LYS 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D TRP* 3.7 5.9 - - - -
541D ALA* 2.9 43.1 + - + +
566D ARG* 1.3 77.4 - - - +
568D LEU* 1.3 71.5 + - - +
569D LEU* 3.8 13.0 + - + +
574D GLN* 3.0 34.1 - - - +
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Residues in contact with LEU 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538D TRP* 3.8 29.4 - - + +
539D VAL 3.6 15.9 - - - +
540D TRP* 3.7 43.3 - - + -
567D LYS* 1.3 83.6 + - - +
569D LEU* 1.3 67.8 + - - +
570D GLU* 3.8 38.1 + - + +
574D GLN* 3.9 4.9 - - - +
670D ALA* 5.2 1.3 - - + -
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Residues in contact with LEU 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539D VAL* 2.8 49.3 + - + +
541D ALA* 4.1 10.5 - - + -
567D LYS* 4.0 30.1 - - + +
568D LEU* 1.3 82.0 - - - +
570D GLU* 1.3 62.5 + - - +
571D MET 3.8 0.4 - - - -
574D GLN* 3.8 26.9 - - + +
575D ALA* 4.2 18.2 - - + -
577D PHE* 4.3 7.6 - - + -
587D LEU* 3.9 15.7 - - + -
669D ILE* 3.4 21.4 - - - +
670D ALA* 4.6 0.9 - - - +
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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