Contacts of the helix formed by residues 624 - 643 (chain r) in PDB entry 6FF7
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 ARG 624 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590r PRO* 6.0 0.2 - - - +
619r LEU* 4.3 5.8 - - + +
622r ASP* 3.0 11.1 - - + +
623r ASP* 1.3 77.7 - - - +
625r GLY* 1.3 65.8 + - - +
626r PRO* 3.3 0.9 - - - -
627r VAL* 3.1 24.9 + - + +
628r LEU* 4.0 2.3 + - - +
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Residues in contact with GLY 625 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619r LEU 3.3 18.0 + - - -
620r LEU* 3.5 15.5 - - - -
622r ASP 2.7 18.7 + - - -
623r ASP 3.0 1.6 - - - -
624r ARG* 1.3 78.2 - - - +
626r PRO* 1.3 60.3 - - - +
627r VAL 3.0 1.4 + - - -
628r LEU* 3.1 9.1 + - - +
629r GLU* 3.1 19.4 + - - +
892r GLN* 5.5 2.0 - - - -
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Residues in contact with PRO 626 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623r ASP 4.2 8.8 - - - +
624r ARG 3.2 0.8 - - - -
625r GLY* 1.3 73.1 - - - +
627r VAL* 1.3 52.7 + - - +
629r GLU* 3.3 11.5 - - + +
630r ALA* 2.7 33.6 + - - +
892r GLN* 4.8 4.0 - - - +
893r MET* 4.2 25.2 - - + +
896r LYS* 4.0 26.7 - - + -
900r MET* 6.0 1.6 - - + +
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Residues in contact with VAL 627 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590r PRO* 4.5 18.6 - - + +
591r GLU* 4.8 11.9 - - + +
594r ASP* 5.3 9.5 - - + +
624r ARG* 3.1 14.8 + - + +
625r GLY 3.0 0.6 + - - -
626r PRO* 1.3 73.9 - - - +
628r LEU* 1.3 55.0 + - - +
629r GLU 3.0 1.1 - - - -
630r ALA* 2.8 9.8 + - - +
631r LEU* 2.8 33.9 + - - +
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Residues in contact with LEU 628 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590r PRO* 4.6 13.3 - - + +
617r ILE* 5.7 3.4 - - - +
619r LEU* 5.5 5.2 - - + -
620r LEU* 5.3 12.1 - - + +
624r ARG 4.0 1.5 + - - +
625r GLY* 3.1 12.6 + - - +
627r VAL* 1.3 79.2 - - - +
629r GLU* 1.3 61.2 + - - +
631r LEU* 3.6 7.5 - - - +
632r VAL* 3.1 26.9 + - - +
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Residues in contact with GLU 629 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625r GLY 3.1 11.6 + - - +
626r PRO* 3.3 15.7 - - + +
627r VAL 3.0 0.4 - - - -
628r LEU* 1.3 78.6 - - - +
630r ALA* 1.3 56.9 + - - +
632r VAL* 4.5 2.4 - - - +
633r ALA* 3.1 32.7 + - - +
891r SER* 5.9 2.7 - - - -
893r MET* 5.2 10.5 - - + -
923r ALA* 5.3 5.4 - - + -
924r TYR* 4.9 23.5 + - + +
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Residues in contact with ALA 630 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594r ASP* 5.7 7.2 - - + -
626r PRO 2.7 14.9 + - - +
627r VAL* 2.8 12.7 + - - +
629r GLU* 1.3 75.2 - - - +
631r LEU* 1.3 66.0 + - - +
633r ALA* 4.0 3.2 - - - +
634r ARG* 3.1 22.9 + - - +
900r MET* 5.4 12.6 - - + -
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Residues in contact with LEU 631 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590r PRO* 5.6 9.2 - - + +
593r TRP* 5.9 5.6 - - + -
594r ASP* 5.8 6.4 - - + +
627r VAL 2.8 14.5 + - - +
628r LEU* 3.6 11.7 - - - +
629r GLU 3.4 0.2 - - - -
630r ALA* 1.3 71.1 - - - +
632r VAL* 1.3 59.8 + - + +
634r ARG* 3.0 8.4 + - - +
635r ALA* 2.9 27.5 + - - +
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Residues in contact with VAL 632 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628r LEU 3.1 14.1 + - - +
629r GLU* 4.5 1.6 - - - +
631r LEU* 1.3 79.6 - - - +
633r ALA* 1.3 63.7 + - - +
635r ALA* 3.1 9.1 + - - +
636r ILE* 2.9 25.2 + - - +
664r PHE 5.5 7.2 - - - +
665r LEU* 6.2 2.2 - - - -
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Residues in contact with ALA 633 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629r GLU 3.1 21.9 + - - +
630r ALA* 4.0 4.7 - - - +
632r VAL* 1.3 75.4 - - - +
634r ARG* 1.3 58.0 + - - +
636r ILE* 3.8 3.0 - - - +
637r ARG* 2.9 35.1 + - - +
919r TRP 5.0 3.4 - - - +
922r TYR* 3.8 34.2 + - + +
923r ALA* 4.6 5.8 - - + +
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Residues in contact with ARG 634 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630r ALA 3.1 11.4 + - - +
631r LEU* 3.0 10.8 + - - +
633r ALA* 1.3 79.9 - - - +
635r ALA* 1.3 56.6 + - - +
637r ARG* 3.8 4.3 - - - +
638r ASN* 2.9 34.3 + - - +
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Residues in contact with ALA 635 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631r LEU 2.9 13.7 + - - +
632r VAL* 3.5 11.7 - - - +
634r ARG* 1.3 77.6 - - - +
636r ILE* 1.3 62.1 + - - +
638r ASN* 3.5 5.7 - - - +
639r ILE* 3.0 23.2 + - - +
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Residues in contact with ILE 636 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632r VAL 2.9 16.0 + - - +
633r ALA* 3.9 4.9 - - - +
635r ALA* 1.3 74.1 - - - +
637r ARG* 1.3 66.1 + - - +
639r ILE* 2.9 18.9 + - - +
640r GLU* 3.2 11.7 + - - +
664r PHE 5.4 7.6 - - - +
666r ARG* 6.0 6.1 - - + -
922r TYR* 5.1 8.1 - - + +
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Residues in contact with ARG 637 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633r ALA 2.9 22.7 + - - +
634r ARG* 4.0 4.0 - - - +
636r ILE* 1.3 73.5 - - - +
638r ASN* 1.3 60.5 + - - +
640r GLU* 3.6 17.3 + - - +
641r MET* 3.7 7.1 + - - +
918r ASN 6.0 0.4 - - - +
919r TRP* 5.4 10.3 - - + -
922r TYR* 4.6 13.2 - - + +
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Residues in contact with ASN 638 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634r ARG 2.9 20.1 + - - +
635r ALA* 3.5 6.7 - - - +
637r ARG* 1.3 75.3 - - - +
639r ILE* 1.3 65.6 + - - +
640r GLU 3.2 1.8 - - - -
641r MET* 3.0 16.7 + - - +
642r THR* 3.1 15.9 + - - -
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Residues in contact with ILE 639 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635r ALA 3.0 13.5 + - - +
636r ILE* 2.9 11.7 + - - +
638r ASN* 1.3 76.0 - - - +
640r GLU* 1.3 56.7 + - - +
642r THR* 4.5 2.2 - - - +
643r GLN* 2.8 32.4 + - - -
644r GLU 3.9 19.3 - - - +
645r ASP* 4.9 8.3 - - + -
646r VAL* 5.5 4.5 - - + +
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Residues in contact with GLU 640 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636r ILE 3.2 9.7 + - - +
637r ARG* 3.7 13.7 - - - +
638r ASN 3.2 0.6 - - - -
639r ILE* 1.3 78.6 - - - +
641r MET* 1.3 60.9 + - - +
643r GLN* 4.3 4.3 + - - +
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Residues in contact with MET 641 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637r ARG 3.7 8.0 + - - +
638r ASN* 3.0 9.9 + - - +
640r GLU* 1.3 81.5 - - - +
642r THR* 1.3 62.1 + - - +
643r GLN* 3.5 2.3 + - - +
1578r THR* 3.5 22.7 - - - +
1579r THR* 6.0 1.3 - - - -
1581r ALA* 4.9 5.2 - - - +
1582r ALA* 4.7 22.0 - - + +
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Residues in contact with THR 642 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638r ASN 3.1 14.8 + - - -
639r ILE* 4.4 1.6 - - - -
641r MET* 1.3 76.8 - - - +
643r GLN* 1.3 63.2 + - - +
644r GLU* 2.9 27.8 + - - +
1578r THR* 5.3 10.7 - - - -
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Residues in contact with GLN 643 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639r ILE 2.8 16.0 + - - -
640r GLU 4.3 4.2 + - - +
641r MET 3.3 4.6 - - - +
642r THR* 1.3 77.0 - - - +
644r GLU* 1.3 59.2 + - - +
645r ASP* 3.7 4.2 + - - +
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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