Contacts of the helix formed by residues 623 - 642 (chain A) in PDB entry 1TF5
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 LEU 623 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A VAL* 3.7 35.0 - - + +
620A SER* 3.1 37.9 - - - +
621A GLU 3.9 1.5 + - - +
622A ASN* 1.3 73.2 - - - +
624A ARG* 1.3 67.9 + - - +
625A GLU* 3.2 2.9 - - - -
626A ILE* 2.9 43.2 + - + +
627A VAL* 2.9 12.7 + - + +
709A ARG* 3.8 9.1 - - - +
712A GLU* 3.4 14.6 - - + +
713A LYS* 4.0 21.3 - - - +
716A VAL* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 624 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A ASN* 3.2 7.1 + - - +
623A LEU* 1.3 76.9 - - - +
625A GLU* 1.3 54.4 + - - +
627A VAL* 3.1 34.4 + - - +
628A GLU* 2.7 52.9 + - - +
631A ILE* 4.4 3.4 - - - +
696A TYR* 3.0 71.2 - - + +
699A LYS* 6.4 0.2 - - - +
708A MET* 4.1 8.2 - - - +
709A ARG* 3.6 20.4 - - - +
712A GLU* 2.8 34.1 + - - -
775A VAL* 3.7 22.2 - - - +
776A MET* 3.9 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A ASN* 4.1 7.0 + - - +
623A LEU 3.2 1.7 - - - -
624A ARG* 1.3 78.3 - - - +
626A ILE* 1.3 68.2 + - + +
628A GLU* 3.6 9.6 + - - +
629A ASN* 2.5 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 626 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A GLU* 6.3 3.1 - - + -
617A VAL* 5.7 8.7 - - + +
620A SER* 5.2 2.9 - - - +
622A ASN 5.3 2.2 - - - +
623A LEU* 2.9 37.6 + - + +
625A GLU* 1.3 86.2 - - + +
627A VAL* 1.3 63.2 + - + +
629A ASN* 3.4 7.3 + - - +
630A MET* 3.1 38.0 + - + +
716A VAL* 5.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 627 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LEU* 2.9 16.9 + - + +
624A ARG* 3.1 24.4 + - - +
626A ILE* 1.3 74.4 - - + +
628A GLU* 1.3 66.2 + - - +
630A MET* 3.1 9.7 + - - +
631A ILE* 3.0 32.1 + - + +
712A GLU* 3.6 27.4 - - + -
716A VAL* 4.3 17.9 - - + -
771A VAL* 3.9 18.8 - - + +
775A VAL* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 628 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A ARG* 2.7 41.0 + - + +
625A GLU* 3.6 7.7 + - - +
627A VAL* 1.3 72.8 - - - +
629A ASN* 1.3 60.2 + - - +
631A ILE* 3.1 14.2 + - + +
632A LYS* 2.9 32.9 + - + +
689A MET* 4.8 2.9 - - - +
693A ILE* 3.1 28.0 - - + +
696A TYR* 3.1 37.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 629 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A GLU* 2.5 37.2 + - - +
626A ILE* 3.5 10.1 - - - +
628A GLU* 1.3 78.3 - - - +
630A MET* 1.3 57.4 + - + +
632A LYS* 3.2 11.8 - - - +
633A SER* 3.0 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A ILE* 3.1 29.5 + - + +
627A VAL* 3.1 10.3 + - - +
629A ASN* 1.3 74.0 - - + +
631A ILE* 1.3 61.9 + - + +
633A SER* 3.7 2.4 + - - -
634A SER* 3.0 28.9 + - - -
716A VAL* 5.1 9.4 - - - -
767A ILE* 3.4 22.0 - - + +
768A GLU* 2.9 69.3 - - + +
771A VAL* 3.8 24.0 - - + -
772A ALA 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A ARG* 4.4 7.4 - - - +
627A VAL* 3.0 28.2 + - + +
628A GLU* 3.1 16.8 + - + +
630A MET* 1.3 73.0 - - - +
632A LYS* 1.3 58.8 + - - +
634A SER* 3.1 5.9 + - - -
635A LEU* 2.7 34.0 + - - +
665A TYR* 3.5 29.6 - - + -
689A MET* 3.6 20.2 - - + -
692A ILE* 4.2 8.5 - - + -
772A ALA* 4.2 20.6 - - + +
775A VAL* 5.3 1.3 - - + -
776A MET* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A GLU* 2.9 17.2 + - + +
629A ASN* 3.2 15.7 - - - +
631A ILE* 1.3 77.9 - - - +
633A SER* 1.3 54.0 + - - +
635A LEU* 3.0 3.0 + - - +
636A GLU* 2.8 34.9 + - - +
685A LEU* 3.8 15.5 - - + +
686A GLU* 2.9 36.4 + - - -
689A MET* 3.4 42.0 - - + +
693A ILE* 6.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A ASN* 3.0 15.9 + - - +
630A MET 3.9 2.2 - - - -
632A LYS* 1.3 76.7 - - - +
634A SER* 1.3 63.4 + - - +
636A GLU* 3.3 10.9 + - - +
637A ARG* 3.2 34.0 + - - +
768A GLU* 3.8 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A MET 3.0 20.8 + - - -
631A ILE 3.3 3.8 - - - -
633A SER* 1.3 78.0 - - - +
635A LEU* 1.3 62.2 + - - +
637A ARG* 3.3 17.6 + - - +
638A ALA* 3.2 16.6 + - - +
665A TYR* 2.5 25.9 + - - -
768A GLU 4.2 1.3 - - - -
769A ASP* 2.7 29.8 + - - +
772A ALA* 3.8 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A ILE 2.7 20.0 + - - +
632A LYS 3.4 3.8 - - - +
634A SER* 1.3 70.1 - - - +
636A GLU* 1.3 61.4 + - - +
638A ALA* 2.9 5.1 + - + +
639A ILE* 2.8 55.4 + - + +
661A ILE* 3.8 27.1 - - + -
665A TYR* 3.4 17.4 + - + -
685A LEU* 4.0 14.4 - - + +
688A ILE* 3.8 33.0 - - + -
689A MET* 3.7 27.6 - - + -
692A ILE* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A LYS 2.8 13.3 + - - +
633A SER* 3.3 13.9 + - - +
635A LEU* 1.3 75.9 - - - +
637A ARG* 1.3 58.4 + - + +
639A ILE* 3.8 5.0 - - - +
640A ALA* 2.9 31.1 + - + +
645A ARG* 6.2 1.6 - - - +
685A LEU* 4.4 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A SER* 3.2 22.3 + - - +
634A SER* 3.6 14.5 - - - +
635A LEU 3.2 0.6 - - - -
636A GLU* 1.3 81.3 - - + +
638A ALA* 1.3 58.2 + - - +
640A ALA* 3.8 5.1 - - - +
641A ALA* 2.9 29.8 + - - +
765A GLU* 3.5 51.3 + - - +
768A GLU* 2.7 32.0 + - - +
769A ASP* 3.2 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A SER 3.2 12.0 + - - +
635A LEU* 2.9 20.1 + - + +
637A ARG* 1.3 77.8 - - - +
639A ILE* 1.3 61.9 + - - +
641A ALA* 3.2 19.1 + - - +
642A TYR* 3.3 8.7 + - - +
657A LEU* 3.6 8.3 - - - +
660A LEU* 4.9 15.9 - - + +
661A ILE* 4.6 13.0 - - + -
665A TYR* 4.5 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A LEU* 2.8 46.2 + - + +
636A GLU* 3.8 4.7 - - - +
638A ALA* 1.3 71.0 - - - +
640A ALA* 1.3 66.0 + - - +
642A TYR* 2.8 13.0 + - - -
643A THR* 2.9 35.9 + - + +
657A LEU* 3.4 18.2 - - + -
681A PRO* 4.5 13.7 - - + +
684A MET* 4.0 21.3 - - + +
685A LEU* 3.4 41.5 - - + +
688A ILE* 4.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A GLU* 2.9 22.3 + - + +
637A ARG* 3.8 6.7 - - - +
639A ILE* 1.3 77.0 - - - +
641A ALA* 1.3 62.7 + - - +
643A THR* 3.1 26.3 + - - +
644A PRO* 4.1 2.4 - - - +
645A ARG* 4.2 28.6 + - - +
681A PRO* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A ARG 2.9 19.3 + - - +
638A ALA* 3.2 11.2 - - - +
640A ALA* 1.3 79.4 - - - +
642A TYR* 1.3 73.6 + - + +
643A THR 3.4 1.3 + - - -
644A PRO* 4.3 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A ALA 3.3 4.0 + - - +
639A ILE 2.8 10.7 + - - +
641A ALA* 1.3 92.2 - - + +
643A THR* 1.3 60.6 + - - +
644A PRO* 3.4 9.8 - - - +
653A LYS* 4.3 6.8 - - - +
654A LEU 4.0 21.5 - - - +
655A ASP* 4.9 4.6 - - - +
656A GLY* 3.5 15.3 - - - -
657A LEU* 2.9 54.3 - - + -
660A LEU* 4.2 18.9 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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