Contacts of the helix formed by residues 628 - 642 (chain D) in PDB entry 5MKE
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 THR 628 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C SER* 5.0 11.2 - - - +
245C ASN* 6.2 0.4 - - - -
247C TYR* 3.8 5.6 - - + -
248C TYR* 3.4 37.0 - - + +
382D ILE* 4.5 17.6 - - + +
383D ILE* 5.5 4.9 - - + -
616D TYR* 4.8 0.2 - - - -
626D PHE 3.1 2.6 + - - -
627D SER* 1.3 78.2 - - - +
629D PHE* 1.3 53.2 + - - +
630D GLN* 3.1 8.5 - - - +
631D GLU* 2.5 62.1 + - - +
632D CYS 3.5 0.9 + - - -
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Residues in contact with PHE 629 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C SER* 5.1 4.0 - - - -
1005C CHS 4.4 52.0 - - + +
609D LEU* 3.5 34.3 - - + -
612D ALA* 4.0 7.0 - - + -
613D GLN* 3.7 35.4 - - + -
616D TYR* 3.8 40.0 - + + -
627D SER 3.7 2.0 - - - -
628D THR* 1.3 70.7 - - - +
630D GLN* 1.3 69.9 + - - +
632D CYS* 3.1 15.2 + - + +
633D ILE* 3.4 9.3 + - + -
1010D PLM 4.5 17.0 - - + +
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Residues in contact with GLN 630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A GLU* 6.0 0.4 + - - -
654A ARG* 5.7 3.6 + - - +
380D TRP* 5.1 8.7 - - - -
382D ILE* 4.0 30.1 + - - +
628D THR* 2.7 13.3 + - - +
629D PHE* 1.3 79.7 - - - +
631D GLU* 1.3 62.1 + - + +
633D ILE* 2.5 43.7 + - + +
634D PHE* 3.5 11.3 + - + -
1009D PLM 2.8 38.1 + - + +
1010D PLM 4.7 18.4 - - + +
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Residues in contact with GLU 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A GLU* 6.1 6.7 - - + -
247C TYR* 5.5 2.4 - - - -
248C TYR* 5.2 3.1 + - - -
382D ILE* 5.1 5.7 - - - +
625D ASP* 3.5 39.5 + - - +
626D PHE 4.5 1.9 + - - +
628D THR* 2.5 36.4 + - - +
630D GLN* 1.3 78.5 - - + +
632D CYS* 1.3 55.5 + - - +
634D PHE* 2.9 32.1 + - + +
635D THR* 2.9 14.7 + - - +
638D ARG* 5.9 0.2 + - - -
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Residues in contact with CYS 632 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D ALA* 3.8 24.3 - - + +
616D TYR* 4.5 10.8 - - - -
625D ASP 4.0 4.9 - - - -
626D PHE* 3.2 27.4 - - + -
627D SER* 2.6 42.8 - - - -
628D THR 3.5 0.4 + - - -
629D PHE* 3.1 15.1 + - + +
630D GLN 3.1 0.6 + - - -
631D GLU* 1.3 76.9 - - - +
633D ILE* 1.3 62.9 + - - +
634D PHE 3.2 0.2 - - - -
635D THR* 4.0 3.6 - - - +
636D GLN* 3.3 22.0 + - - +
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Residues in contact with ILE 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608D PHE* 3.3 39.3 - - + -
609D LEU* 3.5 30.7 - - + -
612D ALA* 4.1 3.8 - - + +
629D PHE* 3.4 6.5 + - + +
630D GLN* 2.5 32.1 + - + +
632D CYS* 1.3 75.3 - - - +
634D PHE* 1.3 75.0 + - + +
636D GLN* 3.4 8.7 - - - +
637D PHE* 2.9 30.9 + - + -
1009D PLM 4.8 16.4 - - + -
1010D PLM 6.2 3.8 - - + -
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Residues in contact with PHE 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A PHE* 4.7 17.3 - + + -
650A GLU* 5.5 7.0 - - + -
654A ARG 5.6 2.0 - - - -
658A PRO* 3.7 34.1 - - + -
659A ILE* 4.5 2.2 - - - -
661A PHE* 4.4 15.4 - + + -
662A THR* 3.1 27.8 - - - -
630D GLN* 3.7 25.8 - - + -
631D GLU* 2.9 20.0 + - + +
633D ILE* 1.3 84.5 - - + +
635D THR* 1.3 50.7 + - - +
636D GLN 2.8 4.7 - - - -
637D PHE* 2.4 33.7 + + - +
638D ARG* 2.7 16.8 + - + +
1009D PLM 5.0 24.2 - - + -
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Residues in contact with THR 635 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625D ASP* 2.5 51.7 + - + +
626D PHE* 3.6 28.0 - - + -
631D GLU* 2.9 9.6 + - - +
632D CYS* 4.1 4.7 - - - -
634D PHE* 1.3 74.3 - - - +
636D GLN* 1.3 57.0 + - - +
637D PHE 3.4 0.2 - - - -
638D ARG* 3.7 21.5 + - + -
639D ILE* 3.4 31.1 + - + +
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Residues in contact with GLN 636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607D ILE 3.8 0.4 + - - -
608D PHE* 2.2 86.5 + - + +
611D TYR* 3.6 12.3 - - - +
612D ALA* 3.1 26.8 - - + +
626D PHE* 6.1 1.1 - - + -
632D CYS 3.3 15.4 + - - +
633D ILE* 3.4 2.6 - - - +
634D PHE 2.8 1.0 + - - -
635D THR* 1.3 77.3 - - - +
637D PHE* 1.3 59.4 + - - +
639D ILE* 4.5 2.9 - - - -
640D ILE* 3.9 4.7 + - - +
660D TYR* 5.1 7.9 - - - +
664D PHE* 3.7 31.2 - - + -
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Residues in contact with PHE 637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A PHE* 4.6 13.0 - + + -
662A THR* 3.8 34.3 - - + -
665A VAL* 4.4 22.1 - - + +
666A PHE* 5.0 19.7 - + + -
670A PHE* 5.6 7.2 - + - -
604D PHE* 4.9 10.3 - + - -
605D PHE* 6.4 1.8 - + - -
608D PHE* 3.4 26.2 - + - -
633D ILE* 2.9 37.0 - - + -
634D PHE* 2.4 27.6 + + - +
636D GLN* 1.3 67.0 - - - +
638D ARG* 1.3 65.7 + - - +
639D ILE 3.0 2.7 - - - -
640D ILE* 2.9 27.4 - - + +
641D LEU* 3.1 9.1 + - - +
1009D PLM 5.6 3.8 - - + -
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Residues in contact with ARG 638 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A ILE* 5.4 2.8 + - + -
646A PHE* 4.9 30.6 - - + +
647A ALA* 5.7 5.4 - - - +
661A PHE* 5.0 14.1 - - + -
625D ASP* 3.4 34.2 + - - +
631D GLU* 5.9 0.4 + - - -
634D PHE 2.7 17.9 + - - +
635D THR* 3.7 21.6 + - + +
636D GLN 3.6 0.4 - - - -
637D PHE* 1.3 72.9 - - - +
639D ILE* 1.3 50.6 + - + +
641D LEU* 3.5 8.1 + - + +
642D GLY 2.5 38.9 + - - +
643D ASP* 2.6 48.6 + - - +
644D ILE* 5.1 3.8 - - + +
645D ASN* 4.7 12.5 + - - +
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Residues in contact with ILE 639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641C LEU* 3.7 22.7 - - + +
626D PHE* 4.8 6.7 - - + -
635D THR* 3.4 28.5 + - + +
636D GLN* 5.0 1.6 - - - +
637D PHE 2.9 1.8 + - - -
638D ARG* 1.3 74.0 - - + +
640D ILE* 1.3 62.0 + - - +
641D LEU 2.9 1.7 - - - -
642D GLY* 2.5 27.0 + - - -
644D ILE* 3.3 29.8 - - + -
649D ILE* 4.6 19.5 - - + -
660D TYR* 5.3 9.2 - - + +
661D PHE* 4.5 17.3 - - + -
664D PHE* 4.2 25.8 - - + -
665D VAL* 5.2 1.8 - - + -
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Residues in contact with ILE 640 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665A VAL* 6.5 1.1 - - + -
669A PHE* 4.1 27.6 - - + -
670A PHE* 4.9 6.3 - - + -
641C LEU* 4.8 9.3 - - - +
604D PHE* 6.2 1.3 - - + -
608D PHE* 5.6 2.0 - - + -
636D GLN 3.9 6.1 - - - +
637D PHE* 2.9 33.0 - - + +
639D ILE* 1.3 77.4 - - - +
641D LEU* 1.3 61.6 + - + +
664D PHE* 4.5 13.9 - - + -
665D VAL* 6.1 1.1 - - - -
669D PHE* 4.2 26.8 - - + -
672D LEU* 3.3 42.8 - - + -
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Residues in contact with LEU 641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A ILE* 3.8 29.4 - - + +
640A ILE* 4.9 8.1 - - - +
641A LEU 4.6 7.7 - - - +
642A GLY* 3.8 27.6 - - - -
643A ASP 4.8 1.1 - - - +
644A ILE* 4.7 14.8 - - + -
661A PHE* 4.8 9.4 - - + -
665A VAL* 3.6 29.8 - - + -
669A PHE* 5.9 8.7 - - + -
641C LEU* 4.6 9.1 - - - +
637D PHE 3.1 11.7 + - - +
638D ARG* 3.5 11.0 - - + +
639D ILE 2.7 5.4 + - - -
640D ILE* 1.3 78.6 - - + +
642D GLY* 1.3 63.8 + - - +
643D ASP* 5.6 2.2 - - + -
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Residues in contact with GLY 642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A GLY* 6.1 0.7 - - - -
641C LEU* 3.7 16.4 - - - -
642C GLY* 6.1 0.7 - - - -
638D ARG 2.5 24.2 + - - +
639D ILE 2.5 16.2 + - - -
641D LEU* 1.3 80.5 - - - +
643D ASP* 1.3 71.6 + - - +
644D ILE* 2.9 15.6 + - - +
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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