Contacts of the helix formed by residues 672 - 689 (chain A) in PDB entry 5FWP
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 ASP 672 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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670A LEU* 3.1 3.4 - - - +
671A GLU* 1.3 91.3 - - + +
673A PRO* 1.4 57.4 - - - +
674A GLN* 3.4 20.1 + - - +
675A THR* 2.6 60.3 + - + +
676A HIS* 3.5 2.4 + - - +
492B GLU* 5.3 2.7 - - + +
493B GLN* 5.8 3.9 - - - +
496B ASN* 3.5 27.8 + - - +
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Residues in contact with PRO 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A SER* 5.3 2.9 - - - +
670A LEU* 3.6 40.7 - - + +
671A GLU 3.9 1.3 - - - +
672A ASP* 1.4 89.3 - - - +
674A GLN* 1.3 56.3 + - - +
676A HIS* 3.2 5.2 + - + +
677A SER* 3.0 28.4 + - - -
493B GLN* 5.3 19.7 - - + +
664B LEU* 4.6 9.6 - - + +
665B SER* 3.8 27.9 - - - +
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Residues in contact with GLN 674 (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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672A ASP* 2.9 14.2 + - - +
673A PRO* 1.3 80.2 - - - +
675A THR* 1.3 57.8 + - + +
677A SER* 2.6 29.5 + - - -
678A ASN* 2.8 47.7 + - - +
681A TYR* 4.8 2.6 - - - -
496B ASN* 3.6 29.8 - - + +
497B SER* 4.7 1.0 - - - -
498B ALA* 4.1 16.2 + - - +
501B GLU* 5.6 3.6 - - - +
586B SER* 5.3 4.8 + - - -
587B SER* 4.7 15.8 + - - -
665B SER* 4.6 14.2 + - - +
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Residues in contact with THR 675 (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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660A GLU* 5.2 5.2 + - - -
672A ASP* 2.6 46.4 + - - +
674A GLN* 1.3 75.3 - - + +
676A HIS* 1.3 65.8 + - - +
678A ASN* 3.3 16.5 + - - +
679A ARG* 3.0 28.5 + - - +
682A ARG* 4.4 4.0 + - - -
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Residues in contact with HIS 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A LEU* 3.8 14.6 - - + -
660A GLU* 2.6 40.8 + - + +
661A THR* 3.8 26.5 - - + +
664A LEU* 3.6 19.5 - - + +
670A LEU* 3.7 24.2 - - + -
672A ASP 3.5 0.8 + - - +
673A PRO* 3.2 11.6 + - + +
674A GLN 3.2 0.2 - - - -
675A THR* 1.3 83.1 + - - +
677A SER* 1.3 61.4 + - - +
679A ARG* 3.1 11.9 + - - +
680A ILE* 3.1 42.1 + - + +
664B LEU* 4.5 9.4 - - + -
676B HIS* 4.8 0.6 + - - -
680B ILE* 4.5 3.8 - - - +
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Residues in contact with SER 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A PRO 3.0 11.9 + - - -
674A GLN* 2.6 37.2 + - - -
676A HIS* 1.3 74.1 - - - +
678A ASN* 1.3 59.4 + - - +
680A ILE* 3.1 7.3 + - - +
681A TYR* 2.8 41.2 + - - -
661B THR* 3.5 27.1 - - - -
665B SER* 3.7 17.0 + - - -
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Residues in contact with ASN 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A GLN* 2.8 50.8 + - - +
675A THR* 3.4 20.3 - - - +
676A HIS 3.1 0.4 - - - -
677A SER* 1.3 73.9 + - - +
679A ARG* 1.3 59.6 + - - +
681A TYR* 3.1 14.9 + - - +
682A ARG* 2.8 47.4 + - + +
586B SER 5.5 2.8 - - - +
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Residues in contact with ARG 679 (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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653A ASP* 4.6 13.3 + - - +
656A VAL* 3.7 15.7 - - - +
657A LEU* 3.9 32.5 - - - +
660A GLU* 2.7 43.3 + - - -
675A THR* 3.0 15.6 + - - +
676A HIS* 3.4 16.8 + - - +
678A ASN* 1.3 75.3 - - - +
680A ILE* 1.3 57.2 + - + +
682A ARG* 3.1 32.2 + - + +
683A MET* 2.8 44.1 + - + +
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Residues in contact with ILE 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A LEU* 5.3 0.9 - - + -
676A HIS* 3.1 42.8 + - + +
677A SER* 3.1 6.9 + - - +
679A ARG* 1.3 76.1 - - + +
681A TYR* 1.3 57.2 + - - +
683A MET* 3.1 21.9 + - + +
684A ILE* 2.8 49.7 + - + +
657B LEU* 4.4 11.2 - - + -
661B THR* 3.5 39.9 - - + +
664B LEU* 6.0 0.4 - - + -
676B HIS* 4.6 10.8 - - + +
680B ILE* 4.8 11.4 - - + -
683B MET* 5.9 2.2 - - + -
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Residues in contact with TYR 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A GLN* 4.8 1.6 - - - -
677A SER* 2.8 42.6 + - - -
678A ASN* 3.4 16.6 - - - +
680A ILE* 1.3 72.4 - - - +
682A ARG* 1.3 57.3 + - + +
684A ILE* 3.2 7.9 + - + +
685A LYS* 2.8 40.6 + - - +
586B SER 5.7 0.9 - - - -
587B SER* 3.5 26.0 + - - -
588B PRO* 3.9 28.9 - - + -
589B CYS* 3.7 18.9 + - - -
634B ILE* 3.9 9.1 - - + +
658B LEU* 3.7 30.7 - - + -
661B THR* 4.0 20.2 - - + +
662B ALA* 4.2 7.6 - - - -
665B SER* 4.8 1.6 + - - -
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Residues in contact with ARG 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A THR 4.4 3.6 + - - -
678A ASN* 2.8 33.5 + - + +
679A ARG* 3.1 46.5 + - + +
681A TYR* 1.3 77.4 - - + +
683A MET* 1.3 57.8 + - + +
685A LYS* 3.3 14.3 + - + +
686A LEU* 3.0 35.2 + - + +
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Residues in contact with MET 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A LEU* 3.8 37.5 - - + -
679A ARG* 2.8 36.4 + - + +
680A ILE* 3.5 22.4 - - + +
682A ARG* 1.3 73.0 - - + +
684A ILE* 1.3 61.1 + - + +
686A LEU* 3.3 16.8 + - + +
687A GLY* 3.0 23.2 + - - -
680B ILE* 5.5 4.0 - - + -
683B MET* 6.0 7.0 - - + -
684B ILE* 5.9 1.8 - - - -
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Residues in contact with ILE 684 (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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680A ILE* 2.8 38.1 + - + +
681A TYR* 3.4 10.5 - - + +
682A ARG 3.2 0.2 - - - -
683A MET* 1.3 73.9 - - + +
685A LYS* 1.3 60.2 + - - +
687A GLY* 3.0 4.3 + - - +
688A LEU* 2.8 45.5 + - + +
634B ILE* 4.1 13.0 - - + -
654B LEU* 3.5 31.2 - - + -
657B LEU* 3.9 15.3 - - + -
658B LEU* 3.4 28.3 - - + -
683B MET* 6.1 0.4 - - - -
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Residues in contact with LYS 685 (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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681A TYR* 2.8 24.3 + - - +
682A ARG* 3.5 13.9 - - + +
684A ILE* 1.3 76.0 - - - +
686A LEU* 1.3 58.7 + - + +
688A LEU 3.2 0.5 + - - -
689A GLY 2.9 9.0 + - - -
690A ILE* 2.8 61.3 + - + -
588B PRO* 5.7 1.8 - - - -
632B HIS* 5.2 10.7 + - - -
633B PRO* 5.3 10.5 - - - +
634B ILE* 3.7 30.7 - - + -
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Residues in contact with LEU 686 (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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682A ARG* 3.0 23.2 + - + +
683A MET* 3.4 19.7 - - + +
684A ILE 3.2 0.2 - - - -
685A LYS* 1.3 77.5 - - + +
687A GLY* 1.3 62.0 + - - +
689A GLY* 3.2 13.1 + - - -
690A ILE 5.9 0.2 - - - -
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Residues in contact with GLY 687 (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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683A MET 3.0 13.2 + - - -
684A ILE* 3.0 5.3 + - - -
686A LEU* 1.3 77.2 - - - +
688A LEU* 1.3 63.0 + - - +
689A GLY 3.6 0.3 + - - -
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Residues in contact with LEU 688 (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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684A ILE* 2.8 38.4 + - + +
685A LYS 3.2 0.4 + - - +
687A GLY* 1.3 78.1 - - - +
689A GLY* 1.3 61.9 + - - +
690A ILE* 3.5 34.5 + - + +
634B ILE* 4.1 12.6 - - + +
637B THR* 4.1 28.5 + - + +
638B LEU* 5.7 0.4 - - + -
641B LYS* 5.1 10.8 - - + -
651B VAL* 6.4 1.3 - - + -
654B LEU* 3.7 24.0 - - + -
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Residues in contact with GLY 689 (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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685A LYS 2.9 4.1 + - - -
686A LEU* 3.2 11.3 + - - -
687A GLY 3.3 1.6 + - - -
688A LEU* 1.3 79.0 - - - +
690A ILE* 1.3 62.3 + - - +
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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