Contacts of the helix formed by residues 641 - 656 (chain f) in PDB entry 5T0J
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 641 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285f ALA* 5.9 3.1 - - + -
287f LEU* 5.3 7.9 - - + -
596f ASP* 5.0 2.0 - - - -
597f PRO* 3.8 33.9 - - + -
600f LEU* 3.6 25.2 - - + +
639f THR* 3.0 6.8 + - - +
640f VAL* 1.3 79.8 - - + +
642f VAL* 1.3 58.4 + - + +
643f SER 3.1 0.2 - - - -
644f PHE* 2.9 37.8 + - + +
645f LEU* 3.1 15.2 + - - +
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Residues in contact with VAL 642 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600f LEU* 5.9 1.6 - - + -
632f VAL 4.8 3.1 - - - +
633f ALA* 4.1 28.6 - - + +
635f ALA 3.7 15.0 - - - +
637f LEU 3.5 12.1 - - - +
638f LEU* 3.8 17.7 - - + -
639f THR* 3.2 31.4 - - - +
641f LEU* 1.3 77.6 - - + +
643f SER* 1.3 60.2 + - - +
644f PHE 3.3 0.2 - - - -
645f LEU* 3.3 34.0 - - + +
646f ASP* 3.3 12.0 - - - +
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Residues in contact with SER 643 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280f TYR* 4.1 18.2 + - - -
283f SER* 2.3 36.5 + - - -
284f GLY 5.4 0.2 - - - -
285f ALA* 4.9 2.4 - - - +
289f CYS* 5.7 0.2 - - - -
638f LEU* 5.3 3.8 - - - -
640f VAL* 2.9 18.6 + - - -
642f VAL* 1.3 81.7 - - - +
644f PHE* 1.3 56.7 + - - +
646f ASP* 2.7 28.3 + - - +
647f VAL* 3.3 10.9 - - - +
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Residues in contact with PHE 644 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285f ALA* 4.5 14.3 - - + +
287f LEU* 3.5 32.3 - - + -
288f ALA* 4.3 7.9 - - + -
597f PRO* 6.0 1.6 - - + -
600f LEU* 3.7 31.6 - - + -
601f PHE* 6.1 6.5 - + - -
604f ARG* 5.8 2.5 - - + -
640f VAL 3.5 1.4 + - - -
641f LEU* 2.9 29.8 + - + +
643f SER* 1.3 79.9 - - - +
645f LEU* 1.3 62.9 + - - +
647f VAL* 3.2 5.7 - - - +
648f ARG* 3.0 71.2 + - + +
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Residues in contact with LEU 645 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600f LEU* 4.3 23.6 - - + -
604f ARG* 3.1 65.0 - - + +
629f MET* 4.6 3.8 - - - +
632f VAL* 3.7 24.7 - - + +
633f ALA* 4.9 2.2 - - + -
641f LEU 3.1 7.3 + - - +
642f VAL* 3.3 37.0 - - + +
644f PHE* 1.3 80.7 - - + +
646f ASP* 1.3 83.2 + - + +
648f ARG* 3.1 9.4 + - - -
649f ASN* 3.4 3.1 + - - +
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Residues in contact with ASP 646 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273f TYR* 3.4 17.7 + - - +
629f MET* 3.8 35.5 - - + +
633f ALA* 4.9 6.1 - - - +
642f VAL 3.3 16.2 - - - +
643f SER* 2.7 27.2 + - - +
645f LEU* 1.3 86.3 - - + +
647f VAL* 1.3 77.2 + - - +
649f ASN* 2.8 18.1 - - - +
650f ILE* 3.8 2.6 - - - +
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Residues in contact with VAL 647 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273f TYR* 4.6 4.0 - - + +
285f ALA* 6.3 0.7 - - + -
288f ALA* 3.7 25.4 - - + +
289f CYS* 4.4 17.3 - - - -
292f VAL* 3.7 27.8 - - + -
643f SER 3.3 13.7 - - - +
644f PHE* 3.2 19.1 - - - +
646f ASP* 1.3 85.2 + - - +
648f ARG* 1.3 61.1 + - - +
649f ASN 3.6 0.2 - - - -
650f ILE* 3.1 20.1 - - + +
651f ILE* 3.1 15.5 - - - +
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Residues in contact with ARG 648 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287f LEU* 5.0 2.2 - - - +
288f ALA* 4.1 4.9 - - - +
604f ARG* 3.7 22.2 - - + +
605f LEU* 5.4 3.1 - - - +
644f PHE* 3.0 55.9 + - + +
645f LEU* 3.1 7.5 + - - +
647f VAL* 1.3 75.6 - - - +
649f ASN* 1.3 67.1 + - - +
650f ILE 3.1 2.0 - - - -
651f ILE* 3.0 33.8 + - - +
652f LEU* 4.3 8.0 + - - +
688f GLY 4.6 6.7 + - - -
691f VAL 5.1 2.8 + - - -
692f ASP* 3.2 46.1 + - - +
694f VAL 6.0 1.2 - - - -
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Residues in contact with ASN 649 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604f ARG* 3.3 40.5 - - - +
607f GLN* 4.3 15.7 - - + +
608f GLY* 5.5 4.3 - - - +
625f ASP* 4.1 18.3 + - - +
629f MET* 3.4 24.3 - - - +
645f LEU 3.4 2.5 + - - -
646f ASP* 2.8 26.0 - - - +
648f ARG* 1.3 76.3 - - - +
650f ILE* 1.3 63.6 + - - +
651f ILE 3.4 0.2 - - - -
652f LEU* 4.6 7.1 - - - +
653f GLY* 3.3 21.0 + - - -
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Residues in contact with ILE 650 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273f TYR* 3.8 24.0 - - + +
274f LEU* 5.3 0.4 - - + -
292f VAL* 3.8 30.3 - - + +
296f VAL* 5.9 0.5 - - - +
622f TYR* 3.3 30.5 - - + +
629f MET* 3.9 4.5 - - + -
646f ASP 3.8 5.4 - - - +
647f VAL* 3.1 34.1 - - + +
649f ASN* 1.3 91.9 + - - +
651f ILE* 1.3 65.5 + - + +
652f LEU 3.5 0.2 - - - -
653f GLY* 3.6 2.2 - - - -
654f LYS* 3.0 39.9 + - + +
655f SER 3.9 0.5 + - - -
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Residues in contact with ILE 651 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288f ALA* 3.3 30.1 - - + +
291f ILE* 3.6 28.8 - - + +
292f VAL* 3.8 16.9 - - + +
647f VAL 3.1 22.1 + - - +
648f ARG* 3.0 32.4 + - - +
650f ILE* 1.3 81.6 - - - +
652f LEU* 1.3 61.7 + - + +
655f SER* 3.0 23.6 + - - -
692f ASP* 4.3 11.2 - - - +
694f VAL 4.7 14.4 - - - +
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Residues in contact with LEU 652 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605f LEU 5.9 1.1 - - - +
608f GLY* 3.8 37.0 - - - +
611f HIS* 4.1 11.6 - - + +
612f LEU* 4.3 13.7 - - + -
613f GLY* 4.3 13.5 + - - -
648f ARG* 5.0 7.4 - - - +
649f ASN* 4.6 5.6 - - - +
651f ILE* 1.3 81.9 - - + +
653f GLY* 1.3 72.6 + - - +
655f SER* 3.4 14.7 + - - -
656f HIS* 4.0 4.2 + - - -
660f TYR* 4.2 17.5 - - - +
694f VAL 5.9 2.7 - - - +
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Residues in contact with GLY 653 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611f HIS* 4.4 13.2 - - - -
616f THR* 4.8 0.9 - - - +
622f TYR* 6.4 0.4 - - - -
625f ASP* 6.2 0.2 - - - -
649f ASN 3.3 23.4 + - - -
650f ILE* 4.2 0.7 - - - -
651f ILE 3.3 0.6 - - - -
652f LEU* 1.3 85.7 - - - +
654f LYS* 1.3 56.9 + - - +
656f HIS* 2.5 39.3 + - - -
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Residues in contact with LYS 654 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268f THR* 2.4 41.6 + - - +
269f GLN* 3.2 41.9 - - - +
273f TYR* 5.1 10.5 - - + -
274f LEU* 6.3 2.0 - - + -
292f VAL* 6.4 0.4 - - + -
296f VAL* 3.6 12.8 - - + +
616f THR* 3.4 27.8 + - + +
622f TYR* 3.5 37.3 - - + +
650f ILE* 3.0 44.0 + - + +
653f GLY* 1.3 79.5 - - - +
655f SER* 1.3 61.1 + - - +
656f HIS* 3.6 1.1 - - - -
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Residues in contact with SER 655 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268f THR* 4.0 0.7 - - - +
291f ILE 6.1 0.4 - - - -
292f VAL 5.4 1.6 - - - -
295f GLY* 4.5 10.1 - - - +
296f VAL* 4.0 20.9 - - - +
650f ILE 3.9 0.4 + - - -
651f ILE 3.0 23.3 + - - -
652f LEU* 3.4 12.8 + - - -
653f GLY 3.4 0.2 - - - -
654f LYS* 1.3 80.8 - - - +
656f HIS* 1.3 83.0 + - - +
657f TYR* 3.2 22.9 - - - -
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Residues in contact with HIS 656 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267f LEU* 5.8 0.7 - - - -
268f THR* 3.5 32.8 - - - +
295f GLY 6.0 0.2 - - - -
611f HIS* 4.2 2.9 - + - -
613f GLY* 3.4 30.4 - - - +
614f LYS 3.0 26.9 - - - -
615f GLY* 3.2 26.9 + - - +
616f THR* 3.6 18.6 - - + +
652f LEU 4.0 2.8 + - - -
653f GLY 2.5 27.8 + - - -
654f LYS* 3.8 3.7 - - - -
655f SER* 1.3 88.6 + - - +
657f TYR* 1.3 64.4 + - + +
658f VAL* 2.7 26.4 + - - +
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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