Contacts of the helix formed by residues 555 - 574 (chain A) in PDB entry 6QVC
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 HIS 555 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A PHE* 5.1 16.1 - + - +
342A PRO* 4.7 14.1 - - + +
343A PHE* 3.2 35.8 - + + -
351A PHE* 4.4 13.3 - + - -
520A LEU* 6.0 4.2 - - + +
523A GLY* 3.5 31.4 - - - -
524A TYR* 6.4 1.6 - + - -
526A VAL* 4.9 5.6 - - + -
527A ILE* 3.7 20.9 - - + +
552A GLN 5.2 0.6 + - - -
553A ILE 3.5 0.8 - - - -
554A ALA* 1.3 86.3 - - + +
556A ILE* 1.3 61.1 + - - +
558A PRO* 3.6 6.3 - - + -
559A MET* 3.3 33.0 + - + +
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Residues in contact with ILE 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A PHE* 3.5 46.2 - - + -
553A ILE* 3.2 33.4 - - + +
554A ALA 2.9 13.0 + - - +
555A HIS* 1.3 70.2 - - - +
557A LEU* 1.3 77.2 + - + +
558A PRO* 3.7 0.6 - - - +
559A MET* 3.2 9.7 - - + +
560A MET* 3.0 50.4 + - + +
283B LEU* 5.6 0.7 - - + -
331B ALA* 6.2 4.3 - - + -
548B GLU* 4.2 19.7 - - + +
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Residues in contact with LEU 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PHE* 5.2 0.7 - - + -
554A ALA 4.9 2.0 - - - +
556A ILE* 1.3 92.5 - - + +
558A PRO* 1.4 72.4 - - + +
560A MET* 3.7 10.0 - - - +
561A VAL* 3.0 34.4 + - - +
282B PRO* 6.0 2.7 - - + -
310B THR* 4.6 5.1 + - - +
313B ALA* 4.3 11.0 - - + +
314B PHE* 3.9 44.4 - - + +
317B ARG* 4.6 4.7 - - + -
329B ILE* 3.6 44.9 - - + +
330B THR 6.1 0.7 - - - -
331B ALA* 6.4 1.3 - - - -
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Residues in contact with PRO 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PHE* 3.6 27.6 - - + -
348A LEU* 4.6 12.3 - - + -
351A PHE* 3.6 33.9 - - + +
527A ILE* 5.2 2.7 - - + -
555A HIS* 3.6 17.5 - - + +
556A ILE 3.7 0.4 - - - +
557A LEU* 1.4 99.9 - - + +
559A MET* 1.3 55.7 + - - +
561A VAL* 3.7 7.1 - - + +
562A ALA* 2.9 30.0 + - - +
314B PHE* 6.2 2.5 - - + -
329B ILE* 5.5 4.9 - - + -
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Residues in contact with MET 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A VAL* 4.9 10.5 - - + -
527A ILE* 3.7 34.0 - - + +
530A ALA* 4.4 16.2 - - + -
543A ALA* 3.8 27.1 - - + +
546A CYS* 4.6 4.9 - - - -
547A PHE* 4.0 30.5 - - + -
550A THR* 5.3 2.7 - - + -
552A GLN 5.6 1.8 - - - +
553A ILE* 6.1 0.7 - - - -
555A HIS* 3.3 31.0 + - + +
556A ILE* 3.2 20.0 - - + +
558A PRO* 1.3 78.6 - - - +
560A MET* 1.3 60.6 + - + +
562A ALA* 4.0 3.2 - - - +
563A VAL* 2.9 34.8 + - - +
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Residues in contact with MET 560 (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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543A ALA* 5.1 9.0 - - + -
544A VAL* 5.8 1.3 - - + -
547A PHE* 4.6 4.0 - - + -
556A ILE* 3.0 45.8 + - + +
557A LEU* 3.7 5.6 - - - +
558A PRO 3.3 0.4 - - - -
559A MET* 1.3 79.7 - - + +
561A VAL* 1.3 62.1 + - - +
563A VAL* 3.4 5.3 + - - +
564A ILE* 3.0 33.3 + - + +
282B PRO* 3.9 27.4 - - - -
283B LEU* 3.7 41.5 - - + +
306B PHE* 4.3 19.7 - - + -
310B THR* 3.7 16.2 - - - +
548B GLU* 4.4 3.1 - - - +
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Residues in contact with VAL 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 6.6 0.2 - - + -
557A LEU 3.0 22.4 + - - +
558A PRO* 3.7 7.0 - - + +
560A MET* 1.3 76.1 - - - +
562A ALA* 1.3 58.4 + - - +
564A ILE* 3.2 6.1 + - - +
565A LEU* 2.9 45.0 + - + +
310B THR* 4.3 15.7 - - + +
311B PHE* 6.0 5.2 - - + -
314B PHE* 4.4 29.4 - - + -
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Residues in contact with ALA 562 (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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351A PHE* 4.3 13.5 - - + +
354A ILE* 4.7 8.5 - - + -
355A GLY* 3.8 19.0 - - - +
527A ILE* 5.2 6.1 - - + +
531A ALA* 4.5 10.4 - - + +
558A PRO 2.9 17.8 + - - +
559A MET* 4.0 5.4 - - - +
561A VAL* 1.3 77.1 - - - +
563A VAL* 1.3 58.0 + - - +
565A LEU* 3.4 10.4 + - - +
566A ALA* 3.0 30.5 + - - +
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Residues in contact with VAL 563 (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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530A ALA* 4.0 13.2 - - + +
531A ALA* 3.9 27.3 - - + +
534A GLY* 5.3 4.7 - - - -
535A ALA 5.6 0.2 + - - -
539A THR 4.1 1.3 - - - +
540A VAL* 4.0 23.3 - - + -
543A ALA* 3.7 26.2 - - + +
559A MET 2.9 21.8 + - - +
560A MET* 3.7 5.4 - - - +
561A VAL 3.3 0.2 - - - -
562A ALA* 1.3 76.0 - - - +
564A ILE* 1.3 57.8 + - + +
566A ALA* 3.4 3.7 + - - +
567A ASN* 2.9 48.9 + - - +
306B PHE* 5.8 0.7 - - + -
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Residues in contact with ILE 564 (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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540A VAL* 3.9 19.3 - - + -
560A MET 3.0 18.0 + - - +
561A VAL* 3.2 4.2 + - - +
563A VAL* 1.3 73.8 - - + +
565A LEU* 1.3 59.7 + - + +
567A ASN* 3.7 6.7 - - + +
568A MET* 3.0 39.0 + - + +
306B PHE* 3.6 27.6 - - + -
307B PHE* 3.6 34.5 - - + +
310B THR* 3.6 28.5 - - + -
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Residues in contact with LEU 565 (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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351A PHE 5.7 0.2 - - - -
352A ALA* 4.5 24.9 - - + +
355A GLY* 4.4 3.1 - - - -
356A ILE* 3.7 28.0 - - + -
561A VAL* 2.9 36.5 + - + +
562A ALA* 3.6 10.8 - - - +
563A VAL 3.3 0.2 - - - -
564A ILE* 1.3 77.2 - - - +
566A ALA* 1.3 61.0 + - - +
568A MET* 3.3 23.1 - - + +
569A VAL* 3.1 26.5 + - - +
307B PHE* 6.5 0.2 - - + -
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Residues in contact with ALA 566 (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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355A GLY* 3.8 21.3 - - - +
359A GLY* 4.0 9.7 - - - +
531A ALA* 4.0 12.8 - - + +
535A ALA* 3.7 23.3 - - + +
562A ALA 3.0 17.0 + - - +
563A VAL 3.9 3.6 - - - +
565A LEU* 1.3 76.5 - - - +
567A ASN* 1.3 58.7 + - - +
569A VAL* 3.5 3.8 + - - +
570A ALA* 2.9 30.8 + - - +
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Residues in contact with ASN 567 (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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534A GLY 2.8 29.5 - - - +
535A ALA* 3.8 1.2 - - - -
538A HIS* 4.2 6.9 - - + -
539A THR 2.5 30.5 + - - +
540A VAL* 3.4 13.4 - - + +
563A VAL* 2.9 36.0 + - - +
564A ILE* 3.7 6.9 - - + +
565A LEU 3.2 0.4 - - - -
566A ALA* 1.3 77.1 - - - +
568A MET* 1.3 58.0 + - - +
570A ALA* 3.8 3.0 - - - +
571A GLN* 2.8 33.4 + - - +
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Residues in contact with MET 568 (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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356A ILE* 6.0 0.2 - - + -
564A ILE* 3.0 36.3 + - + +
565A LEU* 3.3 29.8 - - + +
567A ASN* 1.3 74.7 - - - +
569A VAL* 1.3 64.6 + - + +
571A GLN* 3.8 12.0 - - - +
572A SER* 2.9 29.1 + - - -
115B GLY* 6.5 1.1 - - - -
307B PHE* 4.1 21.5 - - + -
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Residues in contact with VAL 569 (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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356A ILE* 3.9 35.4 - - + +
359A GLY 4.1 0.9 - - - -
360A LEU* 3.9 23.1 - - + +
565A LEU 3.1 17.7 + - - +
566A ALA* 3.8 6.5 - - - +
568A MET* 1.3 79.6 - - + +
570A ALA* 1.3 57.4 + - - +
572A SER* 3.2 8.9 + - - -
573A LEU* 3.0 46.8 + - + +
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Residues in contact with ALA 570 (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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359A GLY 4.8 9.0 - - - +
363A ALA* 5.0 7.9 - - + +
535A ALA* 3.3 31.9 - - + +
538A HIS* 3.6 11.0 - - + +
566A ALA 2.9 18.5 + - - +
567A ASN* 3.8 2.2 - - - +
569A VAL* 1.3 76.2 - - - +
571A GLN* 1.3 60.4 + - - +
573A LEU* 4.4 2.9 - - - +
574A GLN* 2.8 36.1 + - + +
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Residues in contact with GLN 571 (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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538A HIS* 3.7 16.0 + - + +
567A ASN* 2.8 23.7 + - - +
568A MET* 3.9 11.8 - - - +
570A ALA* 1.3 72.3 - - - +
572A SER* 1.3 63.0 + - - +
574A GLN 4.5 3.6 + - - +
303B TRP* 4.7 23.6 - - - -
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Residues in contact with SER 572 (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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568A MET 2.9 19.8 + - - -
569A VAL* 3.3 8.5 - - - -
570A ALA 3.2 0.2 - - - -
571A GLN* 1.3 78.3 - - - +
573A LEU* 1.3 71.3 + - - +
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Residues in contact with LEU 573 (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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360A LEU* 4.6 18.8 - - + -
363A ALA* 4.3 15.7 - - + -
569A VAL* 3.0 37.3 + - + +
570A ALA 3.1 0.9 + - - +
572A SER* 1.3 90.3 - - - +
574A GLN* 1.3 82.2 + - + +
575A PRO* 4.8 0.5 - - - +
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Residues in contact with GLN 574 (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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363A ALA* 3.7 42.6 - - + +
366A VAL* 5.1 4.0 - - + -
367A TYR* 4.2 14.1 - - + +
370A ARG* 2.6 33.6 + - - +
538A HIS* 3.4 5.9 + - - -
570A ALA 2.8 18.4 + - - +
571A GLN 4.5 3.9 - - - +
573A LEU* 1.3 92.3 + - + +
575A PRO* 1.3 77.8 - - + +
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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