Contacts of the strand formed by residues 548 - 558 (chain A) in PDB entry 3HIG
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 ARG 548 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A ASN* 2.9 48.6 + - - +
539A ILE* 3.3 15.1 + - - +
540A THR* 3.2 25.7 + - - +
541A ASN* 4.2 4.0 + - - +
546A ARG 5.7 1.1 - - - +
547A HIS* 1.3 83.0 - - - +
549A VAL* 1.3 66.7 + - - +
550A VAL 4.1 1.0 + - - -
609B TRP* 3.9 31.8 + - + -
1D NAG 3.6 36.4 + - - -
2D NAG 4.4 19.8 - - - +
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Residues in contact with VAL 549 (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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537A GLU 3.6 1.4 - - - +
538A ASN* 3.4 1.7 - - - -
539A ILE* 2.8 46.3 + - + +
541A ASN* 3.9 30.9 - - + +
543A TRP* 5.5 0.7 - - - +
548A ARG* 1.3 76.6 - - - +
550A VAL* 1.3 62.9 + - - +
551A GLN* 3.7 36.3 - - + +
367B MET* 4.0 34.8 - - + +
368B GLN* 6.0 1.6 - - - +
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Residues in contact with VAL 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LEU* 4.0 14.6 - - + -
537A GLU 3.2 7.9 - - - +
538A ASN* 3.7 30.3 - - + +
548A ARG* 4.1 1.4 + - + -
549A VAL* 1.3 72.6 - - - +
551A GLN* 1.3 62.4 + - - +
552A PRO* 4.7 0.2 - - - +
370B LYS* 4.8 8.7 + - - -
605B LEU* 4.2 13.4 - - + +
606B PRO* 3.9 31.6 - - + -
609B TRP* 3.6 37.9 - - + +
1D NAG 4.0 10.3 - - + -
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Residues in contact with GLN 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LEU* 3.3 7.2 - - - -
537A GLU* 2.9 62.9 + - + +
539A ILE* 4.2 7.5 - - - +
549A VAL* 3.7 17.0 - - + +
550A VAL* 1.3 75.8 - - - +
552A PRO* 1.3 74.3 - - + +
553A THR 3.6 0.2 + - - -
359B TYR 4.5 2.2 - - - +
360B GLY* 3.3 3.0 - - - -
361B GLY 2.9 43.6 + - - -
367B MET* 3.1 26.1 - - - +
370B LYS* 6.3 0.7 - - - +
497B HIS* 3.4 8.1 - - - -
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Residues in contact with PRO 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A MET* 3.6 40.2 - - + -
535A LYS 3.9 0.4 - - - +
536A LEU* 4.0 5.6 - - + -
550A VAL 4.7 0.2 - - - +
551A GLN* 1.3 87.2 - - + +
553A THR* 1.3 60.1 + - - +
358B LEU* 4.4 9.6 - - + +
359B TYR 3.3 27.4 - - - +
360B GLY* 3.5 11.9 - - - +
497B HIS* 3.1 18.5 + - - -
509B ILE* 4.0 19.4 - - + +
510B HIS* 5.7 0.7 - - - -
511B THR* 6.1 0.7 - - - +
604B VAL* 5.0 6.3 - - + -
605B LEU* 5.4 5.4 - - + -
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Residues in contact with THR 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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534A MET* 3.4 8.1 - - - +
535A LYS* 2.7 51.2 + - - +
536A LEU 4.9 0.5 - - - -
537A GLU* 3.4 48.6 - - + +
552A PRO* 1.3 78.0 - - - +
554A LEU* 1.3 62.2 + - - +
555A GLU* 5.4 0.7 - - - +
496B ARG* 3.5 22.2 + - - +
497B HIS* 3.5 7.9 - - + -
509B ILE* 4.0 6.5 - - - +
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Residues in contact with LEU 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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532A LEU* 4.0 24.2 - - + -
533A GLN 3.8 2.7 - - - +
553A THR* 1.3 73.8 + - - +
555A GLU* 1.3 64.9 + - - +
556A GLN* 4.3 1.5 + - + -
589A HIS* 6.5 0.2 - - + -
495B LEU 4.2 6.3 - - - +
496B ARG* 2.8 27.6 + - - +
497B HIS* 4.5 0.6 - - - +
498B GLY* 3.7 31.9 - - - +
499B THR* 4.4 2.9 - - - +
509B ILE* 4.1 9.9 - - + -
676B ILE* 3.7 45.1 - - + -
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Residues in contact with GLU 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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531A THR 4.0 0.3 - - - +
532A LEU* 3.2 7.4 - - - +
533A GLN* 2.8 59.0 + - - +
535A LYS* 3.0 42.5 - - + +
553A THR* 3.8 1.3 + - - +
554A LEU* 1.3 74.8 - - - +
556A GLN* 1.3 68.3 + - - +
557A THR* 4.3 10.9 + - - +
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Residues in contact with GLN 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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530A GLN* 4.9 2.0 - - - +
531A THR 3.5 4.9 - - - -
532A LEU* 3.8 17.9 - - + -
554A LEU* 4.3 1.7 + - + -
555A GLU* 1.3 78.9 - - - +
557A THR* 1.3 63.5 + - - +
558A GLN* 4.0 18.2 + - - +
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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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530A GLN* 3.2 7.6 - - - +
531A THR* 2.9 46.8 + - - -
533A GLN* 6.1 0.5 - - - +
555A GLU* 4.3 13.9 + - - +
556A GLN* 1.3 75.6 + - - +
558A GLN* 1.3 73.4 + - - +
559A TYR* 3.4 17.1 - - + +
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Residues in contact with GLN 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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528A SER* 5.8 3.3 - - - -
529A PHE 4.3 3.0 - - - +
530A GLN* 3.1 34.1 + - - +
556A GLN* 4.0 18.1 + - - +
557A THR* 1.3 86.0 - - - +
559A TYR* 1.3 70.3 + - - +
560A SER* 4.3 3.7 + - - +
564A GLN* 5.0 2.8 + - - +
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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