Contacts of the helix formed by residues 620 - 635 (chain A) in PDB entry 3U44
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 ALA 620 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A GLY 3.3 11.1 + - - +
617A TYR* 3.1 19.0 + - - +
618A PHE 3.2 1.1 - - - +
619A GLU* 1.3 77.9 - - - +
621A VAL* 1.3 67.0 + - - +
622A GLU* 3.2 15.5 + - - +
623A VAL* 3.2 10.1 + - + +
624A ALA* 3.0 20.9 + - - +
739A ASN* 4.4 11.2 - - - +
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Residues in contact with VAL 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A GLU 3.5 6.0 + - - +
620A ALA* 1.3 70.9 - - - +
622A GLU* 1.3 72.2 + - + +
624A ALA* 3.3 8.3 + - + +
625A VAL* 3.0 32.1 + - + +
723A TYR* 4.3 1.6 - - - +
736A ARG* 4.6 1.3 - - - +
1131B GLN* 3.5 42.2 - - + +
1132B PHE 4.0 11.2 - - - +
1133B ASP* 3.6 38.1 - - + +
1136B LEU* 5.7 1.3 - - + -
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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 ALA* 4.1 8.7 - - - +
621A VAL* 1.3 82.6 + - + +
623A VAL* 1.3 53.9 + - + +
625A VAL* 3.0 4.2 + - - +
626A ALA* 2.7 34.8 + - - +
723A TYR* 3.0 21.2 + - + +
727A VAL* 3.5 25.4 - - + -
730A MET* 5.1 2.1 - - - +
736A ARG* 2.5 63.8 + - + +
739A ASN* 3.9 13.2 + - - +
740A LEU* 3.7 20.4 - - + -
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Residues in contact with VAL 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A TYR* 3.3 73.1 - - + +
618A PHE* 4.3 9.0 - - + +
620A ALA* 3.2 10.2 + - + +
622A GLU* 1.3 74.6 - - + +
624A ALA* 1.3 63.1 + - - +
626A ALA* 3.7 5.8 - - - +
627A LEU* 3.0 45.4 + - + +
739A ASN* 4.2 12.6 - - + +
740A LEU* 4.6 2.7 - - + -
743A LEU* 5.2 4.9 - - + -
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Residues in contact with ALA 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A PHE 4.7 9.8 + - - +
619A GLU* 5.6 1.3 - - - -
620A ALA 3.0 13.1 + - - +
621A VAL* 3.3 14.4 - - + +
623A VAL* 1.3 77.5 - - - +
625A VAL* 1.3 55.1 + - + +
627A LEU* 3.8 5.7 - - - +
628A SER* 2.6 37.9 + - - -
631A LYS* 5.6 1.0 + - - -
1128B SER* 4.4 23.8 - - - +
1131B GLN* 6.4 0.2 - - + -
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Residues in contact with VAL 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A VAL* 3.0 19.9 + - + +
622A GLU 3.5 5.4 - - - +
624A ALA* 1.3 76.2 - - + +
626A ALA* 1.3 63.8 + - - +
628A SER* 3.1 10.2 - - - -
629A VAL* 3.0 26.8 + - + +
644A SER 4.5 5.2 - - - +
645A VAL* 5.0 1.1 - - - -
648A SER* 3.5 37.0 - - - +
649A PRO* 5.6 1.3 - - + -
650A ILE* 4.1 13.0 - - + -
723A TYR* 3.5 22.4 - - + +
1128B SER 4.9 2.2 - - - +
1131B GLN* 4.1 21.8 - - + +
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Residues in contact with ALA 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A GLU 2.7 19.2 + - - +
623A VAL 3.7 2.0 - - - +
625A VAL* 1.3 72.0 - - - +
627A LEU* 1.3 64.1 + - - +
629A VAL* 2.9 21.6 + - - +
630A LEU* 3.2 15.5 + - - +
718A TYR* 4.1 11.7 - - + +
723A TYR* 4.4 6.0 - - + -
740A LEU* 3.8 17.0 - - + -
743A LEU* 3.7 24.0 - - + -
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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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618A PHE* 4.6 2.0 - - + +
623A VAL* 3.0 39.5 + - + +
624A ALA* 3.8 4.9 - - - +
626A ALA* 1.3 74.6 - - - +
628A SER* 1.3 54.0 + - - +
630A LEU* 2.9 18.0 + - + +
631A LYS* 2.7 54.5 + - + +
743A LEU* 3.7 15.7 - - + -
761A PHE* 4.8 1.1 - - + -
762A LEU* 4.9 8.5 - - + -
765A ILE* 3.6 46.9 - - + -
769A GLN* 4.1 14.1 - - - +
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Residues in contact with SER 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A ALA 2.6 26.1 + - - -
625A VAL* 3.1 15.4 - - - -
627A LEU* 1.3 74.9 - - - +
629A VAL* 1.3 60.5 + - - +
631A LYS* 3.3 18.6 + - - +
632A VAL* 3.1 27.4 + - - +
641A PRO* 3.7 7.2 - - - +
644A SER* 3.1 32.5 + - - -
645A VAL* 3.9 6.3 - - - -
1128B SER* 4.2 7.3 - - - -
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Residues in contact with VAL 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A VAL 3.2 16.2 - - - +
626A ALA* 2.9 11.3 + - - +
628A SER* 1.3 73.8 - - - +
630A LEU* 1.3 65.5 - - + +
632A VAL* 3.1 6.5 + - + +
633A ILE* 3.0 28.9 + - + +
645A VAL* 3.6 23.3 - - + -
650A ILE* 3.9 24.7 - - + -
694A PHE* 5.5 0.7 - - + -
701A TRP* 3.5 35.2 - - + -
717A VAL* 3.8 20.4 - - + -
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Residues in contact with LEU 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A ALA 3.2 10.1 + - - +
627A LEU* 2.9 22.1 + - + +
629A VAL* 1.3 77.3 - - + +
631A LYS* 1.3 57.9 + - - +
633A ILE* 3.2 20.7 + - + +
634A ASP* 2.9 25.2 + - - +
710A VAL* 5.1 0.4 - - + -
713A LEU* 4.5 14.4 - - + -
714A ILE* 4.0 37.0 - - + -
717A VAL* 4.8 6.5 - - + -
743A LEU* 4.9 6.1 - - + -
758A LEU* 3.6 16.9 - - + +
761A PHE* 4.1 24.9 - - + -
762A LEU* 4.3 11.0 - - + -
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Residues in contact with LYS 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A ALA 5.6 0.4 + - - -
627A LEU* 2.7 39.0 + - - +
628A SER* 3.4 18.3 + - - +
629A VAL 3.2 0.2 - - - -
630A LEU* 1.3 74.5 - - - +
632A VAL* 1.3 57.3 + - - +
634A ASP* 3.3 1.7 + - - +
635A ASN 2.9 25.8 + - - +
638A GLN* 3.3 26.1 - - - +
641A PRO* 4.1 22.3 - - + +
762A LEU* 4.2 26.2 - - + -
766A GLU* 5.2 13.1 - - - +
769A GLN* 5.3 8.1 - - - +
1128B SER* 6.2 2.2 - - - -
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Residues in contact with VAL 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A SER 3.1 17.4 + - - +
629A VAL* 3.1 7.2 + - + +
631A LYS* 1.3 73.2 - - - +
633A ILE* 1.3 62.9 + - - +
635A ASN 4.0 5.8 - - - -
636A PRO* 3.0 42.3 - - + +
638A GLN* 5.4 1.3 - - + +
641A PRO* 3.6 22.2 - - + +
642A LEU* 3.8 31.2 - - + +
645A VAL* 4.3 7.0 - - + -
671A TYR* 6.0 0.2 - - + -
694A PHE* 4.5 5.4 - - + -
698A LEU* 3.7 27.9 - - + +
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Residues in contact with ILE 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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629A VAL* 3.0 16.7 + - + +
630A LEU* 3.2 13.4 + - + +
632A VAL* 1.3 78.5 - - - +
634A ASP* 1.3 52.5 + - - +
698A LEU* 4.1 5.4 - - + -
701A TRP* 3.4 60.8 - - + +
702A ARG* 2.7 42.2 + - - +
705A SER* 4.1 6.4 + - - +
713A LEU* 3.9 26.0 - - + -
717A VAL* 3.9 17.9 - - + -
758A LEU* 4.2 4.2 - - + +
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Residues in contact with ASP 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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630A LEU 2.9 16.1 + - - +
631A LYS 3.6 3.8 - - - +
633A ILE* 1.3 77.8 - - - +
635A ASN* 1.3 59.2 + - - +
638A GLN* 5.6 0.2 - - - +
702A ARG* 2.9 14.1 + - - -
758A LEU* 3.6 18.2 - - + +
759A PHE* 3.3 37.2 + - - +
762A LEU* 3.7 20.0 - - + +
408B LYS* 2.9 41.2 + - - +
427B ASP* 4.5 1.4 - - - +
816B ARG* 4.4 9.2 + - - -
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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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631A LYS 2.9 14.2 + - - +
632A VAL* 3.5 3.8 - - - -
634A ASP* 1.3 79.4 - - - +
636A PRO* 1.3 61.6 - - - +
637A TYR* 2.8 31.4 + - - +
638A GLN* 3.4 13.9 - - - +
427B ASP* 3.3 31.2 + - - +
430B GLU* 3.0 27.1 + - - +
431B ASN* 3.1 24.4 + - - -
816B ARG* 3.3 23.0 - - - +
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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