Contacts of the strand formed by residues 543 - 558 (chain A) in PDB entry 2W77
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 LEU 543 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A ASN 3.8 0.5 - - - -
539A VAL* 2.9 48.0 + - + +
540A THR* 3.0 25.7 + - + +
542A ASP* 1.3 80.3 - - - +
544A ASN* 1.3 68.2 + - - +
545A LEU* 5.6 3.4 - - + -
575A ALA* 4.4 20.4 - - + -
576A VAL 3.5 9.2 - - - +
577A TYR* 4.0 21.8 - - + -
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Residues in contact with ASN 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASP* 5.2 0.6 + - - -
128A GLY* 3.1 20.2 + - - +
536A ARG* 3.2 36.1 + - + +
537A PHE 3.2 5.1 - - - +
538A ASN* 2.6 35.8 + - - +
541A ASP 5.8 0.2 + - - -
542A ASP 4.6 2.6 - - - -
543A LEU* 1.3 80.7 - - - +
545A LEU* 1.3 60.9 + - - +
546A PHE* 4.1 5.6 + - + -
575A ALA* 3.3 4.5 - - - +
576A VAL* 3.0 47.7 + - + +
578A ASP* 4.9 4.0 + - - -
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Residues in contact with LEU 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ALA 3.6 1.2 - - - +
536A ARG* 3.5 3.6 - - - +
537A PHE* 2.8 45.5 + - + +
539A VAL* 3.8 22.3 - - + +
543A LEU* 5.6 3.8 - - + -
544A ASN* 1.3 73.2 - - - +
546A PHE* 1.3 63.6 + - - +
547A LEU* 4.3 28.0 - - + -
573A VAL* 5.3 6.5 - - + -
574A GLY 3.4 16.6 - - - +
575A ALA* 4.1 11.7 - - + +
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Residues in contact with PHE 546 (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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156A THR* 3.9 17.7 - - + -
158A LEU* 4.2 6.5 - - + -
160A LEU* 3.7 20.2 - - + -
164A GLU 3.9 6.3 - - - -
166A PRO* 3.8 31.4 - - + -
534A THR* 4.0 12.8 - - + -
535A ALA 3.5 4.9 - - - -
536A ARG* 3.4 37.5 - - + -
544A ASN* 4.3 9.6 - - + -
545A LEU* 1.3 76.1 - - - +
547A LEU* 1.3 70.6 + - - +
548A GLY 4.3 0.4 - - - -
572A TYR* 4.0 24.0 - + + -
573A VAL* 3.7 1.9 - - - +
574A GLY* 2.7 44.1 + - - +
575A ALA* 4.7 0.7 - - - -
576A VAL* 4.9 3.8 - - + -
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Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A MET* 4.1 1.2 - - - +
534A THR* 4.4 2.4 - - - +
535A ALA* 2.8 41.6 + - + +
537A PHE* 4.5 19.1 - - + -
545A LEU* 4.2 25.7 + - + -
546A PHE* 1.3 82.1 - - - +
548A GLY* 1.3 56.3 + - - +
572A TYR 3.6 1.3 - - - +
573A VAL* 4.2 27.6 - - + -
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Residues in contact with GLY 548 (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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533A MET* 2.8 16.2 - - - -
534A THR* 4.0 3.6 - - - -
547A LEU* 1.3 74.8 - - - +
549A GLY* 1.3 59.0 + - - -
569A PHE* 4.3 7.0 - - - -
571A PRO* 3.7 2.9 - - - +
572A TYR* 2.9 39.8 + - - +
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Residues in contact with GLY 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 3.7 15.7 - - - +
531A SER 3.9 0.3 - - - +
532A TYR* 3.1 2.4 - - - -
533A MET* 2.9 31.9 + - - +
548A GLY* 1.3 74.3 - - - -
550A ARG* 1.3 60.4 + - - -
551A VAL* 5.8 0.2 - - - +
569A PHE* 4.2 11.4 - - - -
570A ILE 3.0 15.3 - - - -
572A TYR 4.4 0.9 - - - -
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Residues in contact with ARG 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PRO* 5.6 4.4 - - - +
254A GLY 3.4 19.1 - - - +
255A LEU* 3.2 26.6 + - - +
256A LEU* 3.6 18.7 + - - +
257A THR 5.1 1.4 + - - -
258A GLY* 3.6 17.5 - - - -
458A ASP* 5.5 0.2 + - - -
479A SER* 3.0 31.3 + - - -
528A GLN* 4.7 6.7 - - - +
530A GLY* 3.8 12.6 - - - -
531A SER 3.0 12.3 - - - +
532A TYR* 3.3 27.2 - - + +
549A GLY* 1.3 74.6 - - - -
551A VAL* 1.3 61.8 + - - +
552A VAL* 3.5 23.3 - - + +
568A ARG 3.6 0.7 - - - +
569A PHE* 3.5 5.6 - - - -
570A ILE* 2.8 42.3 + - + +
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Residues in contact with VAL 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A LEU 4.1 0.3 - - - +
530A GLY* 3.4 4.2 - - - -
531A SER* 2.6 57.7 + - - +
549A GLY 6.0 0.2 - - - -
550A ARG* 1.3 72.2 - - - +
552A VAL* 1.3 63.8 + - - +
567A GLY* 4.2 23.1 - - - +
568A ARG 3.4 5.2 - - - +
569A PHE* 4.8 13.2 - - + -
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Residues in contact with VAL 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLY* 4.7 1.3 - - - -
259A ALA* 4.8 4.7 - - + +
528A GLN* 3.6 22.9 - - - +
529A LEU 3.5 3.1 - - - +
550A ARG* 3.5 35.4 - - + +
551A VAL* 1.3 82.2 - - - +
553A ASP* 1.3 69.2 + - - +
554A TYR* 4.7 5.4 - - + -
565A GLU 3.7 4.0 - - - +
567A GLY* 3.4 5.9 + - - -
568A ARG* 3.0 37.0 + - - +
570A ILE* 4.1 13.9 - - + -
593A PHE* 3.8 23.8 - - + -
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Residues in contact with ASP 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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527A ARG* 3.3 27.0 + - - +
528A GLN* 3.5 2.6 + - - -
529A LEU* 2.9 47.6 + - + +
552A VAL* 1.3 75.8 - - - +
554A TYR* 1.3 65.6 + - - +
564A ARG* 3.2 38.2 + - - -
565A GLU 3.4 6.0 - - - +
566A SER* 4.5 3.0 - - - -
567A GLY 4.5 6.3 - - - +
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Residues in contact with TYR 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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225A THR* 5.3 2.0 - - + +
227A ARG* 3.2 48.8 + - - +
259A ALA* 3.8 20.6 - - + -
526A THR* 3.7 17.3 - - + +
527A ARG 3.5 3.8 - - - -
528A GLN* 3.4 31.9 - - + -
552A VAL* 4.7 7.9 - - + -
553A ASP* 1.3 78.6 + - - +
555A ARG* 1.3 62.2 + - - +
556A VAL* 3.8 15.9 - - + -
563A ILE* 3.5 2.4 - - + +
564A ARG* 3.4 3.8 - - - -
565A GLU* 3.0 34.7 + - + +
593A PHE* 5.4 1.6 - - + -
594A MET* 3.9 8.3 - - + +
595A PRO* 3.4 35.4 - - + -
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Residues in contact with ARG 555 (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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525A LYS 3.8 0.9 - - - +
526A THR* 3.5 3.3 - - - +
527A ARG* 2.8 67.3 + - + +
553A ASP 4.3 0.2 - - - -
554A TYR* 1.3 75.0 - - - +
556A VAL* 1.3 62.8 + - - +
557A THR* 3.9 22.7 + - - +
562A THR* 4.2 24.1 + - + +
563A ILE 3.3 5.4 - - - +
564A ARG* 3.8 34.8 - - + +
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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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227A ARG* 3.9 19.7 - - - +
524A ASP* 3.9 27.4 - - - +
525A LYS 3.4 7.4 - - - +
526A THR* 4.2 9.2 - - - +
554A TYR* 3.8 22.0 - - + -
555A ARG* 1.3 73.4 - - - +
557A THR* 1.3 62.8 + - - +
561A PRO 4.3 1.0 - - - +
562A THR* 3.4 5.2 + - - -
563A ILE* 2.8 79.3 + - + +
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Residues in contact with THR 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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524A ASP* 3.5 5.8 - - - +
525A LYS* 2.6 69.3 + - + -
555A ARG* 3.9 26.3 + - - +
556A VAL* 1.3 75.6 - - - +
558A GLY* 1.3 58.1 + - - +
560A ASN 5.3 1.1 - - - -
562A THR* 4.0 17.2 + - - +
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Residues in contact with GLY 558 (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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523A ASP* 3.3 20.4 - - - -
524A ASP* 4.5 0.9 - - - -
525A LYS* 5.5 0.9 - - - -
557A THR* 1.3 81.3 - - - +
559A LEU* 1.3 68.2 + - - +
560A ASN 3.3 13.4 + - - +
562A THR 5.8 0.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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