Contacts of the helix formed by residues 620 - 637 (chain A) in PDB entry 5KZW
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 620 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A TRP* 2.8 15.8 + - - +
619A SER* 1.3 73.8 - - - +
621A TRP* 1.3 59.1 + - - +
622A GLU* 3.7 4.6 + - - +
623A GLN* 3.1 32.1 + - - +
624A LEU* 3.1 22.7 + - - +
657A LEU* 3.7 8.0 - - - +
661A TRP* 3.5 7.3 - - - -
1022A SO4 3.3 24.7 - - - -
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Residues in contact with TRP 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A SER* 1.3 69.0 - - - +
622A GLU* 1.3 65.9 + - - +
624A LEU* 3.3 10.5 + - + +
625A ALA* 3.0 24.4 + - - +
654A SER* 4.8 4.2 + - - -
656A GLU* 3.8 14.1 - - + -
657A LEU* 3.5 46.7 - - + +
660A ARG* 3.6 37.7 - - + -
756A LEU 3.6 13.2 - - - +
757A GLN* 3.5 33.2 - - - -
758A ALA* 3.5 39.6 - - + +
1022A SO4 2.9 31.7 + - - +
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Residues in contact with GLU 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A SER* 3.8 6.7 - - - +
621A TRP* 1.3 77.3 - - - +
623A GLN* 1.3 60.9 + - + +
625A ALA* 3.4 6.3 + - - +
626A SER* 2.9 32.3 + - - +
1022A SO4 3.1 23.9 + - - +
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Residues in contact with GLN 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 3.9 26.9 - - - +
285A PRO* 3.5 23.1 + - - +
616A ASP 5.0 0.2 + - - -
617A VAL* 3.8 25.0 - - + +
618A TRP* 3.4 52.5 - - + +
620A SER* 3.1 15.4 + - - +
622A GLU* 1.3 80.8 - - + +
624A LEU* 1.3 67.3 + - - +
626A SER* 3.7 4.6 - - - -
627A SER* 2.9 23.2 + - - -
661A TRP* 3.9 7.6 - - + -
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Residues in contact with LEU 624 (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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620A SER 3.1 13.7 + - - +
621A TRP* 3.5 28.0 - - + +
623A GLN* 1.3 75.2 - - - +
625A ALA* 1.3 61.5 + - - +
627A SER* 2.6 24.5 + - - -
628A VAL* 3.9 4.2 + - - +
657A LEU* 3.7 21.3 - - + -
660A ARG* 4.0 13.9 - - + -
661A TRP* 3.7 51.0 - - + +
664A LEU* 4.0 20.0 - - + -
755A VAL 4.4 1.3 - - - +
756A LEU* 3.9 19.5 - - + -
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Residues in contact with ALA 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A TRP 3.0 13.4 + - - +
622A GLU* 3.7 8.7 - - - +
624A LEU* 1.3 77.3 - - - +
626A SER* 1.3 62.7 + - - +
628A VAL* 3.2 13.5 + - - +
629A PRO* 3.2 10.6 - - - +
742A HIS* 3.7 27.1 - - + +
756A LEU* 4.1 29.4 - - + +
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Residues in contact with SER 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 4.1 29.8 - - - +
265A SER 5.4 2.8 + - - +
622A GLU* 2.9 20.0 + - - +
623A GLN* 3.9 10.3 - - - +
624A LEU 3.3 0.2 - - - -
625A ALA* 1.3 72.9 - - - +
627A SER* 1.3 65.2 + - - +
628A VAL 3.2 0.7 + - - -
629A PRO* 3.5 11.6 - - - +
630A GLU* 3.4 21.4 + - - +
742A HIS* 5.4 0.7 - - - -
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Residues in contact with SER 627 (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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617A VAL* 6.6 0.4 - - - -
623A GLN 2.9 13.8 + - - -
624A LEU* 2.6 21.2 + - - -
626A SER* 1.3 78.3 - - - +
628A VAL* 1.3 61.1 + - - +
630A GLU* 4.4 8.5 - - - -
631A ILE* 3.0 30.0 + - - +
644A ALA* 4.1 14.8 - - - -
661A TRP* 5.0 1.1 - - - -
664A LEU* 3.8 4.5 - - - +
668A TYR* 2.6 35.9 + - - -
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Residues in contact with VAL 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A LEU 4.3 4.0 - - - +
625A ALA 3.2 8.3 + - - +
626A SER 3.2 1.6 - - - -
627A SER* 1.3 79.0 - - - +
629A PRO* 1.3 70.5 - - + +
631A ILE* 3.2 3.9 + - - +
632A LEU* 3.0 32.1 + - + +
664A LEU* 4.1 33.9 - - + -
668A TYR* 5.7 0.7 - - - -
741A ASP 3.2 17.9 - - - +
742A HIS* 4.2 3.8 - - - -
743A GLN 3.9 21.3 - - - +
744A LEU* 4.3 12.6 - - + -
754A PRO* 4.7 2.5 - - + -
756A LEU* 4.4 15.3 - - + -
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Residues in contact with PRO 629 (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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265A SER 3.8 15.3 - - - +
266A PRO* 4.7 2.0 - - + -
267A LEU* 3.7 18.9 - - + +
625A ALA 3.2 14.6 - - - +
626A SER* 3.5 14.6 - - - +
628A VAL* 1.3 93.1 - - + +
630A GLU* 1.3 55.6 + - - +
632A LEU* 3.4 9.0 + - + +
633A GLN* 2.8 30.9 + - - +
741A ASP* 3.3 38.8 - - + +
742A HIS* 4.2 5.8 - - + +
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Residues in contact with GLU 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU* 3.1 32.9 - - - +
263A HIS 4.4 11.2 - - - +
264A LEU* 4.0 21.2 - - + +
265A SER 5.2 1.3 + - - +
285A PRO* 5.4 1.6 - - - +
291A LEU* 4.8 4.4 - - - +
614A THR* 3.4 37.4 + - + +
617A VAL* 5.2 3.5 - - - +
626A SER 3.4 15.7 + - - +
627A SER* 3.9 7.5 - - - +
628A VAL 3.2 1.2 - - - -
629A PRO* 1.3 78.8 - - - +
631A ILE* 1.3 63.2 + - - +
633A GLN* 3.2 7.0 + - + +
634A PHE* 3.2 31.5 + - + -
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Residues in contact with ILE 631 (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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614A THR* 3.8 19.3 - - + -
627A SER* 3.0 26.5 + - - +
628A VAL* 3.9 3.6 - - - +
630A GLU* 1.3 75.6 - - - +
632A LEU* 1.3 64.8 + - + +
634A PHE 3.4 1.6 + - - -
635A ASN* 3.0 28.9 + - - -
642A VAL* 3.6 14.5 - - + +
643A GLY* 3.7 39.9 - - - +
644A ALA 3.9 3.6 - - - +
668A TYR* 3.8 18.6 - - + -
669A PRO* 4.0 22.9 - - + -
724A ALA* 4.2 13.5 - - + -
744A LEU* 5.1 6.3 - - + -
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Residues in contact with LEU 632 (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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267A LEU* 4.1 20.4 - - + -
628A VAL* 3.0 28.7 + - + +
629A PRO* 3.6 4.7 - - + +
631A ILE* 1.3 77.9 - - + +
633A GLN* 1.3 62.4 + - - +
635A ASN* 3.2 7.1 + - - +
636A LEU* 3.1 25.2 + - - +
724A ALA* 3.8 9.8 - - + +
725A ARG 3.5 36.6 - - - +
726A PRO* 4.2 18.7 - - + +
741A ASP* 4.4 7.4 - - - +
743A GLN 3.7 22.4 - - - +
744A LEU* 3.8 14.4 - - + -
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Residues in contact with GLN 633 (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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258A THR* 3.0 23.6 + - - -
259A GLY* 3.0 38.0 + - - +
261A ALA* 4.5 11.2 - - + -
266A PRO 5.3 0.3 - - - +
267A LEU* 3.7 14.7 - - + +
269A LEU* 5.1 2.3 - - - +
629A PRO 2.8 20.7 + - - +
630A GLU* 3.2 9.8 + - + +
632A LEU* 1.3 74.4 - - - +
634A PHE* 1.3 59.5 + - + +
636A LEU* 3.2 13.7 + - - +
637A LEU* 3.1 38.9 + - + +
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Residues in contact with PHE 634 (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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261A ALA* 4.3 10.5 - - + -
262A GLU* 3.5 40.4 - - + -
295A HIS* 3.8 12.3 - + - -
602A THR* 3.7 20.2 - - + -
612A HIS* 3.4 36.6 - + - -
630A GLU* 3.2 33.5 + - + +
633A GLN* 1.3 78.7 - - + +
635A ASN* 1.3 63.8 + - - +
637A LEU* 3.1 12.4 + - + +
638A GLY 3.2 0.3 + - - -
639A VAL* 2.8 57.5 + - + +
642A VAL* 3.8 16.2 - - + -
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Residues in contact with ASN 635 (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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351A VAL* 4.4 2.1 - - - +
355A LEU* 5.2 0.5 - - - +
631A ILE* 3.0 27.1 + - - +
632A LEU 3.5 6.7 - - - +
634A PHE* 1.3 75.9 - - - +
636A LEU* 1.3 60.3 - - + +
638A GLY* 3.1 13.5 + - - -
639A VAL 4.3 2.5 - - - -
640A PRO* 3.3 24.7 + - - +
642A VAL* 3.6 16.8 - - - +
669A PRO* 4.3 0.4 - - - +
721A GLU 5.4 0.7 - - - +
722A THR* 3.5 19.7 - - + +
723A VAL* 3.0 14.2 + - - +
724A ALA* 3.0 51.7 + - - +
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Residues in contact with LEU 636 (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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258A THR* 3.8 32.1 - - + +
267A LEU* 4.2 11.4 - - + -
297A PHE* 4.5 7.7 - - + -
299A LEU* 5.4 4.0 - - + -
351A VAL* 3.6 31.4 - - + +
354A TYR* 4.3 9.4 - - - -
632A LEU 3.1 17.5 + - - +
633A GLN* 3.2 18.8 + - - +
635A ASN* 1.3 75.8 - - + +
637A LEU* 1.3 61.4 + - + +
638A GLY 3.3 1.1 + - - -
722A THR* 4.3 3.4 - - + -
726A PRO* 3.9 14.6 - - + -
728A PHE* 4.3 9.6 - - + -
729A LEU* 3.5 41.7 - - + -
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Residues in contact with LEU 637 (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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259A GLY* 4.9 1.3 - - - -
260A LEU 5.2 0.2 - - - +
261A ALA* 3.4 34.5 - - + +
295A HIS* 3.8 35.1 + - + +
297A PHE* 3.6 42.4 - - + +
354A TYR* 4.1 12.9 + - + -
355A LEU* 4.0 10.0 - - - +
358A VAL* 5.2 0.2 - - - +
605A GLY* 5.1 5.9 + - - -
607A GLY 5.6 0.3 + - - -
633A GLN* 3.1 29.9 + - + +
634A PHE* 3.6 13.5 - - + +
635A ASN 3.1 0.8 - - - -
636A LEU* 1.3 78.0 - - - +
638A GLY* 1.3 60.1 + - - +
639A VAL* 3.4 8.1 + - + +
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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
------------------------------------------------------------
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