Contacts of the helix formed by residues 554 - 574 (chain B) in PDB entry 2X04
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 PRO 554 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B SER 4.4 2.7 - - - +
553B ALA* 1.3 89.2 - - + +
555B PRO* 1.3 76.7 - - + +
556B GLN* 3.4 2.2 - - + +
557B GLU* 2.9 19.4 + - + +
558B GLN* 2.9 19.2 + - - +
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Residues in contact with PRO 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B ALA 3.8 1.5 - - - +
554B PRO* 1.3 87.1 - - + +
556B GLN* 1.3 62.8 + - - +
558B GLN* 3.4 14.6 + - + +
559B LYS* 3.3 24.9 + - - +
590B ASN* 4.9 2.2 + - - +
1398D LEU* 3.7 21.8 - - + +
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Residues in contact with GLN 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B PRO* 3.4 2.7 - - + +
555B PRO* 1.3 78.7 - - - +
557B GLU* 1.3 74.5 + - - +
559B LYS* 3.2 5.4 + - - +
560B GLN* 3.0 44.4 + - - +
1394D PRO* 4.0 9.2 - - - +
1395D TRP* 3.3 22.8 + - - +
1398D LEU* 2.6 31.4 - - - +
1399D GLN* 3.3 41.2 + - + +
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Residues in contact with GLU 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B ALA* 3.8 15.7 - - + -
554B PRO* 2.9 28.4 + - + +
556B GLN* 1.3 85.7 + - - +
558B GLN* 1.3 60.3 + - - +
560B GLN* 3.1 12.4 + - - +
561B MET* 2.8 47.9 + - + +
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Residues in contact with GLN 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B LEU* 3.0 48.5 + - + +
551B ALA* 3.9 12.6 + - - +
553B ALA* 2.8 22.1 + - + +
554B PRO 2.9 19.7 + - - +
555B PRO* 3.7 11.3 - - - +
556B GLN 3.3 0.2 - - - -
557B GLU* 1.3 76.8 - - - +
559B LYS* 1.3 61.5 + - - +
561B MET* 3.3 4.3 + - - +
562B LEU* 3.0 30.1 + - - +
590B ASN* 3.0 29.5 + - - +
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Residues in contact with LYS 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A VAL* 4.4 8.6 - - - +
555B PRO 3.3 12.7 + - - +
556B GLN* 3.2 9.6 + - - +
558B GLN* 1.3 76.5 - - - +
560B GLN* 1.3 57.6 + - - +
562B LEU* 3.3 1.2 + - - -
563B GLY* 2.8 26.2 + - - -
586B LEU* 2.8 43.7 + - + +
587B GLU 4.4 2.8 + - - -
588B ILE 2.8 24.0 + - - -
589B ASP* 4.9 0.6 - - - +
590B ASN* 2.7 32.1 + - - +
593B LEU* 4.2 1.0 - - - +
1389D PHE* 4.6 0.4 - - - -
1395D TRP* 3.9 27.1 - - + -
1398D LEU* 3.6 27.8 - - + +
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Residues in contact with GLN 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556B GLN* 3.0 24.8 + - - +
557B GLU* 3.1 22.4 + - - +
559B LYS* 1.3 77.7 - - - +
561B MET* 1.3 62.2 + - - +
563B GLY* 3.8 0.2 - - - -
564B GLU* 3.0 56.6 + - + +
1389D PHE* 3.6 14.2 - - - -
1392D GLY 4.5 0.8 - - - -
1393D VAL 3.0 27.8 + - - +
1394D PRO* 4.0 4.7 - - - -
1395D TRP* 2.9 27.2 + - - +
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Residues in contact with MET 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B LEU* 4.0 28.0 - - + -
549B MET* 4.7 11.0 - - + +
550B LEU* 3.9 21.1 - - + -
553B ALA* 4.0 26.5 - - + -
557B GLU* 2.8 35.5 + - + +
558B GLN* 3.5 5.8 - - - +
560B GLN* 1.3 77.3 - - - +
562B LEU* 1.3 63.0 + - - +
564B GLU* 4.9 1.3 - - - -
565B ARG* 2.8 38.8 + - - +
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Residues in contact with LEU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B LEU* 3.8 19.7 - - + -
550B LEU* 4.0 14.4 - - + -
558B GLN 3.0 19.8 + - - +
559B LYS* 3.8 4.5 - - - +
561B MET* 1.3 77.2 - - - +
563B GLY* 1.3 57.9 + - - +
565B ARG* 3.2 4.5 + - - +
566B LEU* 2.9 39.3 + - + +
586B LEU* 4.0 9.0 - - + -
590B ASN* 3.4 41.1 - - + +
593B LEU* 3.9 15.9 - - + -
594B LEU* 4.0 19.7 - - - +
597B LEU* 3.8 16.6 - - + +
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Residues in contact with GLY 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559B LYS 2.8 20.8 + - - -
560B GLN 3.3 0.2 + - - -
562B LEU* 1.3 73.9 - - - +
564B GLU* 1.3 61.7 + - - +
566B LEU* 4.4 0.9 - - - -
567B PHE* 2.9 30.3 + - - +
582B THR* 4.3 5.4 - - - -
586B LEU* 3.8 12.9 - - - +
1389D PHE* 3.4 23.3 - - - -
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Residues in contact with GLU 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B LEU* 3.5 25.8 - - + +
560B GLN* 3.0 48.8 + - + +
561B MET* 4.2 5.8 - - - +
562B LEU 3.3 0.2 - - - -
563B GLY* 1.3 77.0 - - - +
565B ARG* 1.3 60.8 + - - +
567B PHE* 5.1 0.2 - - - -
568B PRO* 3.0 23.6 - - - +
1389D PHE* 3.5 7.8 - - - -
1391D PRO* 3.5 12.6 - - - +
1392D GLY* 2.9 35.4 + - - -
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Residues in contact with ARG 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B LEU* 3.9 20.1 - - + +
543B GLY* 2.8 42.2 + - - +
544B SER 4.8 2.4 + - - -
545B LEU* 3.8 32.3 - - - +
549B MET* 5.9 0.8 - - - +
561B MET* 2.8 37.4 + - - +
562B LEU 3.2 3.0 + - - +
563B GLY 3.1 0.6 - - - -
564B GLU* 1.3 88.9 - - - +
566B LEU* 1.3 65.0 + - - +
567B PHE 3.4 0.4 - - - -
568B PRO* 3.5 8.6 - - - +
569B LEU* 3.8 18.9 - - - +
597B LEU* 3.8 23.3 - - + -
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Residues in contact with LEU 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562B LEU* 2.9 31.3 + - + +
563B GLY 4.1 2.5 - - - +
565B ARG* 1.3 75.2 - - - +
567B PHE* 1.3 67.2 + - - +
569B LEU* 3.1 6.9 + - - +
570B ILE* 3.0 36.0 + - + +
582B THR* 4.2 6.3 - - + -
585B LEU* 4.9 6.5 - - + -
586B LEU* 4.1 17.3 - - + -
593B LEU* 4.0 27.4 - - + +
596B MET* 4.6 8.5 - - + -
597B LEU* 3.7 25.4 - - + -
603B LEU* 3.6 30.5 - - + -
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Residues in contact with PHE 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B GLY 2.9 19.7 + - - +
564B GLU 4.8 0.4 - - - +
566B LEU* 1.3 75.8 - - - +
568B PRO* 1.4 64.1 - - + +
570B ILE* 3.2 1.7 + - - +
571B GLN* 2.7 72.6 + - + +
578B ALA* 3.8 9.2 - - + -
579B GLY* 3.7 18.6 - - - -
582B THR* 3.6 20.6 + - - +
1389D PHE* 3.5 37.7 - + + -
1390D HIS* 5.9 0.7 - - - -
1391D PRO* 3.2 33.9 - - + -
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Residues in contact with PRO 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B LEU* 5.6 3.1 - - + -
564B GLU 3.0 28.9 - - - +
565B ARG* 3.5 10.5 - - - +
567B PHE* 1.4 100.1 - - + +
569B LEU* 1.3 62.7 + - + +
571B GLN* 3.5 9.7 + - + +
572B ALA* 3.1 22.3 + - - +
1391D PRO* 5.8 2.7 - - + -
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Residues in contact with LEU 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565B ARG 3.8 16.8 - - - +
566B LEU 3.1 6.6 + - - +
568B PRO* 1.3 77.8 - - + +
570B ILE* 1.3 65.3 + - - +
572B ALA* 3.3 15.8 + - + +
573B MET* 3.4 22.8 - - + +
597B LEU* 4.3 17.7 - - + +
603B LEU* 4.0 24.9 - - + -
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Residues in contact with ILE 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B LEU* 3.0 31.5 + - + +
567B PHE 3.7 2.7 - - - +
569B LEU* 1.3 76.3 - - - +
571B GLN* 1.3 52.5 + - - +
573B MET* 2.9 11.8 + - - +
574B HIS* 2.7 32.2 + - - +
578B ALA* 4.0 13.0 - - - -
581B ILE* 3.8 33.2 - - + -
582B THR* 3.4 25.6 - - - +
585B LEU* 3.7 28.0 - - + -
603B LEU* 4.4 9.0 - - + -
607B VAL* 3.9 17.7 - - + -
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Residues in contact with GLN 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567B PHE* 2.7 47.9 + - + +
568B PRO* 3.8 8.9 - - - +
569B LEU 3.3 0.2 - - - -
570B ILE* 1.3 73.3 - - - +
572B ALA* 1.3 61.7 + - - +
574B HIS 3.9 0.2 - - - -
575B PRO* 3.2 38.4 + - + +
578B ALA* 3.5 24.1 - - + +
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Residues in contact with ALA 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568B PRO 3.1 14.4 + - - +
569B LEU* 3.4 13.9 - - + +
570B ILE 3.2 0.4 - - - -
571B GLN* 1.3 77.4 - - - +
573B MET* 1.3 62.8 + - + +
575B PRO* 4.5 5.6 - - - +
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Residues in contact with MET 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569B LEU* 3.4 21.1 - - + +
570B ILE* 2.9 7.0 + - - +
572B ALA* 1.3 81.0 - - + +
574B HIS* 1.3 81.1 + - + +
575B PRO* 3.7 6.3 - - - +
600B PRO 5.6 1.1 - - - +
603B LEU* 4.1 30.3 - - + -
604B ARG* 4.0 39.5 - - + +
607B VAL* 4.0 21.1 - - + -
1620B SO4 4.5 0.3 + - - -
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Residues in contact with HIS 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570B ILE 2.7 11.0 + - - +
571B GLN 3.5 2.7 - - - -
573B MET* 1.3 85.4 + - + +
575B PRO* 1.3 61.2 - - - +
577B LEU* 4.4 1.8 - - + -
578B ALA* 2.9 30.8 + - - +
581B ILE* 3.7 20.2 - - + -
604B ARG* 5.8 2.7 - - - -
607B VAL* 3.7 24.0 - - + +
608B ASP* 4.7 9.0 - - - -
611B VAL* 3.5 33.0 - - + +
615B GLN* 5.6 2.0 + - - -
1620B SO4 2.6 35.7 - - - +
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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
------------------------------------------------------------
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