Contacts of the helix formed by residues 551 - 564 (chain A) in PDB entry 1V9P
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 GLY 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545A LEU* 4.0 2.2 - - - -
549A GLU 3.5 5.3 + - - -
550A VAL* 1.3 74.9 - - - +
552A GLU* 1.3 56.2 + - - -
553A LEU* 3.1 3.8 - - - -
554A THR* 3.0 11.9 + - - -
555A ALA* 2.7 34.8 + - - +
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Residues in contact with GLU 552 (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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545A LEU* 3.4 25.4 - - + +
551A GLY* 1.3 72.0 - - - -
553A LEU* 1.3 62.8 + - - +
555A ALA* 3.8 0.3 - - - +
556A ARG* 3.2 53.1 + - - +
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Residues in contact with LEU 553 (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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420A GLY* 6.3 2.2 - - - +
551A GLY* 3.1 1.4 - - - -
552A GLU* 1.3 83.7 - - - +
554A THR* 1.3 64.9 + - + +
556A ARG* 4.4 4.6 - - - +
557A ALA* 3.6 16.3 + - - +
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Residues in contact with THR 554 (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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516A PRO 4.3 14.6 - - - +
517A GLY* 4.7 11.4 - - - -
522A LEU* 5.9 3.2 - - - +
549A GLU 4.7 1.2 + - - -
550A VAL* 3.9 8.3 - - - +
551A GLY* 3.0 26.7 + - - +
553A LEU* 1.3 80.4 - - + +
555A ALA* 1.3 66.6 + - - +
557A ALA* 3.0 7.2 + - - +
558A ILE* 2.9 31.0 + - - +
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Residues in contact with ALA 555 (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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541A LEU* 3.9 11.2 - - + -
544A LEU* 3.9 14.7 - - + +
545A LEU* 3.3 34.8 - - + -
550A VAL* 3.8 17.0 - - + -
551A GLY 2.7 13.3 + - - +
552A GLU 3.8 1.3 - - - +
554A THR* 1.3 73.7 + - - +
556A ARG* 1.3 57.7 + - - +
557A ALA 3.0 0.5 + - - -
558A ILE* 3.3 5.2 + - - +
559A LEU* 2.9 30.0 + - - +
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Residues in contact with ARG 556 (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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541A LEU* 2.9 42.0 - - + +
545A LEU* 6.2 0.4 - - - +
552A GLU* 3.2 49.1 + - - +
553A LEU* 4.4 4.6 - - - +
555A ALA* 1.3 79.4 - - - +
557A ALA* 1.3 60.0 + - - +
559A LEU* 3.8 10.9 - - + +
560A GLU* 3.6 16.3 + - - +
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Residues in contact with ALA 557 (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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516A PRO* 3.9 24.2 - - + +
553A LEU 3.6 12.4 + - - +
554A THR* 3.0 13.6 + - - +
555A ALA 3.0 1.0 - - - -
556A ARG* 1.3 75.7 - - - +
558A ILE* 1.3 60.0 + - - +
559A LEU 2.9 0.9 - - - -
560A GLU* 2.6 28.5 + - - +
561A THR* 3.1 10.7 + - - -
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Residues in contact with ILE 558 (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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515A LEU* 5.0 10.1 - - + -
516A PRO* 3.9 29.4 - - + +
518A VAL* 4.5 7.9 - - + +
522A LEU* 4.3 14.8 - - + -
526A LEU* 4.0 28.0 - - + -
536A LEU* 5.3 2.0 - - + -
544A LEU* 4.3 16.2 - - + -
550A VAL* 5.4 4.9 - - + -
554A THR* 2.9 20.3 + - - +
555A ALA* 3.8 5.8 - - - +
557A ALA* 1.3 77.6 - - - +
559A LEU* 1.3 64.5 + - - +
561A THR* 3.3 2.8 + - - -
562A LEU* 2.9 55.0 + - + +
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Residues in contact with LEU 559 (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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539A ALA 3.9 19.1 - - - +
540A SER* 4.4 0.7 - - - -
541A LEU* 4.0 33.0 - - + +
544A LEU* 3.5 23.3 - - + +
555A ALA 2.9 18.6 + - - +
556A ARG* 3.8 13.7 - - + +
557A ALA 2.9 0.2 - - - -
558A ILE* 1.3 79.1 - - - +
560A GLU* 1.3 63.9 + - - +
562A LEU* 4.0 8.0 + - + +
563A LYS* 3.3 51.6 + - - +
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Residues in contact with GLU 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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556A ARG 3.6 9.7 + - - +
557A ALA* 2.6 17.3 + - - +
559A LEU* 1.3 83.6 - - - +
561A THR* 1.3 64.1 + - - +
563A LYS* 3.3 16.6 + - - +
564A ASP* 3.1 19.9 + - - +
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Residues in contact with THR 561 (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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426A PRO* 4.8 15.5 + - - +
428A PRO* 4.8 7.0 - - + -
515A LEU* 3.3 30.5 - - + -
516A PRO* 3.5 23.2 - - + +
557A ALA 3.1 5.9 + - - -
558A ILE 3.8 6.1 - - - -
560A GLU* 1.3 75.7 - - - +
562A LEU* 1.3 58.2 + - - +
564A ASP* 2.7 35.5 + - - +
567A PHE* 3.4 25.1 - - + +
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Residues in contact with LEU 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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515A LEU* 4.2 15.0 - - + -
533A MET* 4.2 13.5 - - + -
536A LEU* 3.8 38.8 - - + +
537A LEU* 3.7 10.9 - - + +
539A ALA* 4.8 5.6 - - + +
544A LEU* 4.8 2.2 - - + -
558A ILE* 2.9 40.5 + - + +
559A LEU* 4.1 10.8 - - + +
561A THR* 1.3 80.7 - - - +
563A LYS* 1.3 61.3 + - + +
564A ASP 4.1 0.9 - - - +
567A PHE* 3.8 28.6 - - + -
568A ARG* 3.0 30.7 + - - +
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Residues in contact with LYS 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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537A LEU 5.7 2.2 - - - +
539A ALA 5.3 4.5 - - - -
559A LEU* 3.3 50.3 + - - +
560A GLU* 3.3 18.4 + - - +
561A THR 3.1 0.8 - - - -
562A LEU* 1.3 78.4 - - + +
564A ASP* 1.3 65.2 + - - +
565A PRO* 3.2 7.6 - - - +
568A ARG* 4.1 19.5 + - - +
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Residues in contact with ASP 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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414A HIS* 2.5 38.8 + - - -
426A PRO* 5.0 3.3 - - - +
427A ASN* 4.5 1.4 + - - -
428A PRO* 3.9 10.8 - - + +
560A GLU 3.1 12.2 + - - +
561A THR* 2.7 27.1 + - - +
563A LYS* 1.3 71.1 - - - +
565A PRO* 1.3 90.2 - - - +
566A ALA* 3.1 18.6 + - - +
567A PHE* 3.0 7.8 + - + +
568A ARG* 3.0 20.3 + - - +
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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
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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