Contacts of the strand formed by residues 602 - 610 (chain A) in PDB entry 3KSS
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 VAL 602 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596A ILE* 3.1 29.2 - - + +
597A MET* 3.6 18.6 - - - +
599A VAL* 3.0 35.7 - - + +
600A PRO 4.4 1.2 - - - +
601A GLU* 1.3 82.9 - - + +
603A ALA* 1.3 63.8 + - - +
605A VAL* 4.5 9.2 - - + -
628A ILE* 4.1 22.9 - - + -
629A GLN 3.5 6.7 - - - +
630A LEU* 4.2 5.4 - - + -
631A LYS* 4.0 7.3 - - - -
645A ILE* 5.5 0.2 - - + -
649A LEU* 5.0 10.3 - - + -
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Residues in contact with ALA 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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597A MET* 3.1 25.8 - - - +
601A GLU 4.0 1.4 + - - -
602A VAL* 1.3 74.1 - - - +
604A ARG* 1.3 65.1 + - + +
629A GLN* 2.4 35.3 + - + +
630A LEU* 4.2 4.7 - - - +
631A LYS* 3.7 25.3 - - + +
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Residues in contact with ARG 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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278A LEU* 6.1 3.1 - - + -
279A ASN* 3.9 11.9 - - - +
322A VAL* 4.1 22.4 - - - +
323A THR* 3.0 45.2 + - - +
324A THR* 4.8 5.8 - - + +
603A ALA* 1.3 83.8 + - + +
605A VAL* 1.3 74.8 + - - +
628A ILE* 4.7 0.2 - - - +
629A GLN* 3.1 50.6 + - + +
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Residues in contact with VAL 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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278A LEU* 3.7 8.3 - - - +
279A ASN* 2.8 35.6 + - - +
324A THR* 4.8 3.0 - - - +
593A ASP* 4.0 24.5 - - - +
596A ILE* 3.9 35.7 - - + -
597A MET* 3.7 23.8 - - - -
602A VAL* 4.5 4.9 - - + -
604A ARG* 1.3 88.0 - - - +
606A PHE* 1.3 69.3 + - - +
626A THR* 5.1 4.5 - - - -
627A THR 3.5 9.4 - - - +
628A ILE* 4.4 8.3 - - + -
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Residues in contact with PHE 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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141A GLU* 5.9 6.7 - - + -
142A TYR 4.6 2.9 - - - -
143A ALA* 3.3 30.3 - - + -
180A VAL* 4.8 15.5 - - + -
276A ALA* 3.9 21.3 - - + -
277A GLU 3.3 17.5 - - - -
278A LEU* 4.9 4.9 - - + -
284A VAL* 5.0 3.6 - - + -
286A GLY* 5.4 2.0 - - - -
324A THR* 3.0 48.0 - - + -
593A ASP* 4.3 0.7 - - - -
605A VAL* 1.3 77.2 - - - +
607A GLY* 1.3 72.6 + - - +
608A LYS* 3.9 8.7 + - + -
625A GLU 4.0 0.2 - - - +
626A THR* 2.9 10.8 - - - -
627A THR* 2.8 42.8 + - - +
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Residues in contact with GLY 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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276A ALA* 3.3 3.5 - - - -
277A GLU 2.6 42.3 + - - +
589A LEU* 3.5 23.7 - - - +
593A ASP* 3.4 12.7 + - - -
606A PHE* 1.3 75.4 - - - +
608A LYS* 1.3 59.5 + - - -
626A THR* 3.5 9.4 - - - -
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Residues in contact with LYS 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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138A TRP* 5.7 7.5 - - + -
180A VAL* 3.8 28.3 - - + -
275A ILE 3.5 3.6 - - - +
276A ALA* 4.5 0.2 - - - +
589A LEU* 3.8 1.7 - - - +
606A PHE* 4.7 7.6 - - + -
607A GLY* 1.3 75.1 - - - +
609A THR* 1.3 61.3 + - - +
610A GLY 2.9 21.2 + - - +
611A LYS 4.4 7.2 - - - +
612A ALA* 4.5 4.3 - - + -
617A ASP* 2.8 28.3 + - - +
625A GLU* 2.7 87.9 + - + +
669A ARG* 4.7 0.6 - - - +
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Residues in contact with THR 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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274A GLY* 3.6 1.0 - - - -
275A ILE* 2.8 34.1 + - - -
585A ALA* 4.1 14.1 + - + +
589A LEU* 3.0 34.0 - - - +
608A LYS* 1.3 72.1 + - - +
610A GLY* 1.3 59.4 + - - +
621A LEU* 2.9 51.8 - - + +
622A GLU 4.4 3.8 - - - +
623A MET 3.5 7.2 - - - +
624A VAL* 4.3 7.5 - - + +
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Residues in contact with GLY 610 (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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273A ARG 4.2 4.5 - - - -
608A LYS* 2.9 27.6 + - - -
609A THR* 1.3 73.9 - - - +
611A LYS* 1.3 62.1 + - - -
617A ASP* 3.1 0.5 - - - +
619A ALA* 2.9 12.9 - - - +
620A PRO 2.9 26.0 + - - -
621A LEU* 4.2 1.1 - - - -
623A MET 3.0 11.5 + - - -
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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