Contacts of the strand formed by residues 601 - 609 (chain A) in PDB entry 1Q2L
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 GLY 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554A LEU 3.4 11.4 - - - -
556A ASN* 4.0 11.4 - - - -
560A MET* 3.2 21.4 - - - +
569A PHE* 4.2 1.6 - - - -
598A ALA* 3.7 3.1 - - - -
599A ASN 2.8 26.3 + - - -
600A ASN* 1.3 75.9 - - - +
602A LEU* 1.3 63.4 + - - -
694A LEU* 4.4 4.0 - - - -
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Residues in contact with LEU 602 (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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552A LEU 3.8 0.7 - - - +
553A ILE* 3.5 1.6 - - - +
554A LEU* 2.7 52.1 + - + +
569A PHE* 3.9 6.7 - - + -
596A THR* 4.1 11.0 - - - -
597A ASN 3.8 7.6 - - - +
601A GLY* 1.3 73.2 - - - -
603A MET* 1.3 73.1 + - - +
604A VAL* 3.6 21.9 - - + +
621A LEU* 4.3 1.1 - - + -
624A TYR* 3.4 35.7 - - + +
625A PHE* 3.6 35.0 - - + -
694A LEU* 3.9 22.2 - - + +
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Residues in contact with MET 603 (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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551A SER* 4.8 16.6 - - - +
552A LEU 3.1 8.3 - - - +
553A ILE* 3.8 28.3 - - + -
596A THR* 3.3 3.8 - - - -
597A ASN* 2.8 66.6 + - - +
599A ASN* 3.5 28.9 - - + +
602A LEU* 1.3 75.9 - - - +
604A VAL* 1.3 67.7 + - - +
605A ASN* 5.6 4.3 - - + -
877A SER* 5.3 13.0 - - - +
880A PHE* 5.3 3.4 - - + -
881A ASP* 6.1 1.6 - - + -
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Residues in contact with VAL 604 (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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550A VAL 3.8 0.9 - - - +
551A SER* 3.4 2.6 - - - -
552A LEU* 2.7 46.8 + - + +
595A SER 3.5 7.6 - - - +
596A THR* 4.4 7.9 - - + -
602A LEU* 3.6 30.1 - - + -
603A MET* 1.3 80.4 - - - +
605A ASN* 1.3 65.2 + - - +
617A PHE* 3.9 21.1 - - + -
620A LEU* 3.5 35.7 - - + -
621A LEU* 3.9 16.6 - - + -
624A TYR* 5.9 0.4 - - + -
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Residues in contact with ASN 605 (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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549A ASP* 2.9 23.2 + - - +
550A VAL 3.3 4.2 - - - +
551A SER* 2.9 25.3 + - - +
593A SER 5.3 0.8 + - - -
594A PHE* 3.0 7.8 - - - +
595A SER* 2.8 50.3 + - - +
597A ASN* 5.7 1.5 + - - +
603A MET* 5.6 5.4 - - + -
604A VAL* 1.3 78.8 - - - +
606A ALA* 1.3 69.5 + - - +
607A ASN* 4.5 4.6 - - - +
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Residues in contact with ALA 606 (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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548A ALA 4.0 0.7 - - - +
549A ASP* 3.4 3.1 - - - -
550A VAL* 2.8 34.3 + - + +
593A SER 3.3 9.6 - - - +
594A PHE* 4.0 9.6 - - + -
605A ASN* 1.3 77.4 - - - +
607A ASN* 1.3 61.3 + - - +
613A LEU* 4.1 17.9 - - + -
616A LEU* 4.4 8.7 - - + -
617A PHE* 3.7 26.7 - - + -
620A LEU* 4.9 0.2 - - + -
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Residues in contact with ASN 607 (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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547A LYS* 5.3 7.1 - - - +
548A ALA 3.5 5.8 - - - -
549A ASP* 3.0 30.8 - - - +
591A GLY 4.0 0.5 - - - +
592A ILE* 3.3 5.7 - - - -
593A SER* 2.9 43.1 + - - +
605A ASN* 4.6 5.2 - - - +
606A ALA* 1.3 76.0 - - - +
608A GLY* 1.3 66.0 + - - +
613A LEU* 4.9 1.1 - - - -
869A LEU* 3.8 12.1 - - - +
870A GLY* 3.7 18.8 + - - +
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Residues in contact with GLY 608 (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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547A LYS* 4.0 12.6 - - - -
548A ALA 3.2 27.8 + - - +
591A GLY 3.2 13.5 - - - -
592A ILE* 3.9 4.9 - - - -
607A ASN* 1.3 85.6 - - - +
609A TYR* 1.3 70.4 + - - +
610A THR* 4.0 0.5 - - - -
613A LEU* 4.2 4.2 - - - +
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Residues in contact with TYR 609 (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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398A ILE* 3.4 31.6 - - + +
402A TYR* 3.6 41.2 + + - +
508A PRO* 4.1 24.5 - - + -
510A ASP 6.0 0.4 - - - +
511A PHE* 3.9 16.8 - + + -
546A PRO* 3.2 21.1 - - + -
547A LYS* 3.7 29.6 + - + +
590A GLY 3.5 21.3 - - - +
591A GLY* 3.5 16.8 + - - -
592A ILE* 3.5 20.8 - - + +
608A GLY* 1.3 73.5 - - - +
610A THR* 1.3 62.9 + - - +
611A GLN 3.6 1.1 - - - +
612A ARG 4.4 1.0 + - - -
613A LEU* 3.7 4.5 + - - +
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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