Contacts of the helix formed by residues 617 - 633 (chain A) in PDB entry 3L4U
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 617 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A PHE* 3.2 34.3 + - - +
614A GLY* 2.8 18.0 + - - -
615A ALA 3.5 0.8 + - - -
616A ASP* 1.3 79.8 - - - +
618A LEU* 1.3 65.4 + - - +
619A LEU* 3.7 4.2 + - - -
620A LEU* 3.1 17.2 + - - +
621A ASN* 3.1 26.7 + - - -
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Residues in contact with LEU 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A GLU* 4.7 3.3 + - - +
585A ARG* 3.6 33.9 - - - +
616A ASP 3.9 0.6 + - - -
617A SER* 1.3 71.2 - - - +
619A LEU* 1.3 58.4 + - - +
621A ASN* 4.6 10.3 - - + +
622A SER* 2.9 30.6 + - - +
722A GLY* 4.2 13.5 - - - +
723A ASP* 3.8 24.7 - - + +
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Residues in contact with LEU 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A GLU* 3.9 20.4 + - + +
584A CYS* 3.8 17.5 - - + +
585A ARG* 3.5 41.7 - - + +
588A MET* 4.8 4.3 - - + -
610A PRO* 3.7 17.5 - - + +
613A PHE* 3.6 49.4 - - + -
617A SER* 3.2 2.7 + - - -
618A LEU* 1.3 79.2 - - - +
620A LEU* 1.3 57.5 + - - +
622A SER* 3.8 1.0 - - - -
623A SER* 2.7 50.3 + - - +
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Residues in contact with LEU 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ASN* 5.1 0.7 - - - +
317A ALA* 3.6 33.9 - - + -
319A LEU* 4.2 11.7 - - + -
610A PRO* 3.9 32.1 - - + +
611A ALA* 4.0 8.1 - - + +
614A GLY 3.5 10.5 - - - +
615A ALA* 3.5 28.0 - - - +
617A SER* 3.1 21.2 + - - +
619A LEU* 1.3 80.7 - - - +
621A ASN* 1.3 58.5 + - - +
623A SER* 3.7 1.5 - - - -
624A ARG* 2.9 42.0 + - + +
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Residues in contact with ASN 621 (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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615A ALA 4.4 6.2 - - - +
616A ASP* 3.8 18.1 + - - +
617A SER 3.1 21.6 + - - +
618A LEU* 3.8 11.0 - - + +
620A LEU* 1.3 76.0 - - - +
622A SER* 1.3 59.3 + - - +
624A ARG* 2.9 29.5 + - - +
625A HIS* 2.9 30.2 + - - +
3001A SO4 5.0 0.9 + - - -
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Residues in contact with SER 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ARG* 4.7 6.3 - - - -
589A GLN* 2.9 38.1 + - - +
618A LEU* 2.9 18.9 + - - -
619A LEU 3.9 2.2 - - - -
621A ASN* 1.3 75.1 - - - +
623A SER* 1.3 65.9 + - - +
625A HIS* 3.2 8.0 + - - +
626A TYR* 3.0 29.3 + - - -
723A ASP* 3.7 21.6 + - - -
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Residues in contact with SER 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.3 5.4 - - - -
585A ARG* 5.7 0.2 - - - -
588A MET* 3.4 48.3 - - - +
589A GLN* 5.8 0.4 - - - +
592A ALA* 5.4 0.3 - - - +
610A PRO* 4.3 12.3 - - - -
619A LEU* 2.7 38.4 + - - +
620A LEU 3.7 3.6 - - - -
622A SER* 1.3 72.1 - - - +
624A ARG* 1.3 56.9 + - - +
626A TYR* 4.1 1.9 - - - +
627A LEU* 2.9 35.6 + - - +
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Residues in contact with ARG 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ALA* 2.7 40.6 + - - +
318A GLN* 3.6 22.4 - - - +
319A LEU* 4.1 12.9 - - + +
320A PRO* 4.1 6.2 - - + +
615A ALA 5.0 2.0 + - - -
620A LEU* 2.9 36.0 + - - +
621A ASN* 2.9 38.6 + - - +
623A SER* 1.3 76.4 - - - +
625A HIS* 1.3 59.1 + - - +
627A LEU* 3.8 1.0 - - - +
628A ASN* 2.9 48.1 + - - +
3001A SO4 4.0 9.5 + - - +
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Residues in contact with HIS 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A ASN 2.9 18.8 + - - +
622A SER* 3.2 8.3 + - - +
624A ARG* 1.3 75.6 - - - +
626A TYR* 1.3 75.3 + + - +
628A ASN* 3.3 5.4 + - - +
629A ILE* 3.2 37.3 + - + +
704A GLU* 2.9 41.3 + - - -
723A ASP 5.3 1.0 + - - -
724A LYS* 4.8 6.5 + - - -
3001A SO4 2.8 39.4 + - - +
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Residues in contact with TYR 626 (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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588A MET 5.2 0.2 - - - +
589A GLN* 4.0 15.5 - - + +
592A ALA* 3.7 21.1 - - + +
593A PHE* 4.0 7.5 - + + -
622A SER* 3.0 33.9 + - - +
623A SER* 4.5 1.3 - - - +
625A HIS* 1.3 84.4 - - - +
627A LEU* 1.3 61.5 + - - +
628A ASN 3.2 0.4 - - - -
629A ILE* 3.3 23.2 + - + +
630A ARG* 2.8 27.4 + - - +
704A GLU* 3.1 18.5 + - - -
723A ASP 3.4 19.1 - - - -
724A LYS* 3.3 14.3 - - - +
725A ILE* 3.2 48.5 + - + -
727A LEU* 3.8 19.5 - - + -
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Residues in contact with LEU 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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294A PHE* 3.9 40.6 - - + -
319A LEU* 4.0 13.2 - - + -
320A PRO* 3.6 28.3 - - + +
588A MET* 4.0 20.9 - - + +
592A ALA* 4.0 19.0 - - + +
597A SER* 4.3 1.3 - - - +
623A SER 2.9 22.0 + - - +
626A TYR* 1.3 76.7 - - - +
628A ASN* 1.3 57.0 + - - +
630A ARG* 3.3 25.7 + - - +
631A TYR* 2.9 36.7 + - + -
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Residues in contact with ASN 628 (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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318A GLN 5.1 1.7 + - - +
320A PRO* 3.4 18.2 - - - +
624A ARG* 2.9 31.7 + - - +
625A HIS 3.5 6.1 - - - +
626A TYR 3.2 0.2 - - - -
627A LEU* 1.3 77.9 - - - +
629A ILE* 1.3 52.1 + - + +
631A TYR* 3.4 1.2 + - - -
632A THR* 2.8 36.9 + - - -
740A PRO* 3.7 30.4 - - + +
741A ASN 4.8 5.5 + - - -
742A THR* 6.2 0.8 - - - +
3001A SO4 3.3 26.4 + - - +
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Residues in contact with ILE 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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593A PHE* 3.9 15.7 - - + -
625A HIS* 3.2 32.4 + - + +
626A TYR* 3.6 33.2 - - + +
628A ASN* 1.3 71.6 - - + +
630A ARG* 1.3 67.5 + - - +
632A THR* 3.1 9.3 + - - -
633A LEU* 3.1 37.4 + - + +
703A TYR* 3.8 35.7 - - + +
704A GLU* 3.9 9.0 - - - +
727A LEU* 4.1 7.2 - - + -
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Residues in contact with ARG 630 (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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292A LEU 2.8 32.8 + - - -
293A GLY 4.5 1.6 + - - -
592A ALA 2.8 45.0 + - - +
593A PHE* 3.9 11.3 - - + +
594A TYR 2.7 22.2 + - - +
595A PRO 3.0 27.1 + - - -
597A SER* 3.7 18.9 - - - +
626A TYR 2.8 16.5 + - - +
627A LEU* 3.4 26.9 - - - +
629A ILE* 1.3 74.6 - - - +
631A TYR* 1.3 73.0 + - - +
633A LEU* 3.1 4.6 + - - +
634A LEU* 3.1 25.4 + - + +
637A LEU* 4.0 12.6 - - - +
674A TRP* 4.0 17.1 - - + -
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Residues in contact with TYR 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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293A GLY* 3.2 10.4 - - - -
294A PHE* 2.9 31.7 + - + -
320A PRO* 3.6 21.5 - - + -
321A TYR 3.4 9.2 + - - -
322A ASP* 2.6 30.1 + - - -
627A LEU* 2.9 27.8 + - + +
628A ASN* 3.8 0.7 - - - +
630A ARG* 1.3 90.7 - - + +
632A THR* 1.3 64.8 + - - +
634A LEU* 3.0 32.2 + - + +
635A PRO* 4.2 2.1 - - - +
738A GLN* 4.0 4.7 - - - +
740A PRO* 3.8 21.2 - - + +
741A ASN 3.4 22.4 - - - -
742A THR 4.3 1.8 - - - -
743A THR 4.2 0.7 - - - -
744A THR* 4.1 13.5 - - + -
747A SER* 4.7 10.1 + - - +
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Residues in contact with THR 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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628A ASN 2.8 20.4 + - - -
629A ILE* 3.1 12.3 + - - -
631A TYR* 1.3 77.3 - - - +
633A LEU* 1.3 57.8 + - + +
635A PRO* 3.5 2.9 - - - +
703A TYR* 3.7 20.2 - - - +
737A THR* 3.1 30.2 - - + -
738A GLN 3.0 38.5 + - - +
739A GLN* 5.6 0.4 - - - -
740A PRO* 3.4 19.2 - - + +
755A ILE* 5.9 0.2 - - + -
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Residues in contact with LEU 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A PHE* 4.9 2.2 - - + -
629A ILE* 3.1 33.6 + - + +
630A ARG 3.1 5.3 + - - +
632A THR* 1.3 74.5 - - - +
634A LEU* 1.3 64.5 + - - +
635A PRO* 3.3 4.3 - - - -
636A TYR* 3.0 14.6 + - + +
637A LEU* 3.0 19.4 + - - +
674A TRP* 3.9 14.4 - - + -
678A LEU* 4.2 27.1 - - + -
703A TYR* 4.1 24.7 - - + +
729A LEU* 5.5 2.5 - - + -
735A PHE* 4.5 19.3 - - + -
736A PRO 4.5 4.7 - - - +
737A THR* 4.0 22.0 - - + -
755A ILE* 4.9 0.9 - - + -
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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