Contacts of the helix formed by residues 551 - 563 (chain S) in PDB entry 1I84
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 551 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549S LYS 5.9 0.4 - - - -
550S ALA* 1.3 74.4 - - - +
552S ASP* 1.3 63.6 - - - +
553S THR* 3.4 13.9 + - - -
554S SER* 2.3 65.2 + - - -
555S PHE 2.6 4.6 + - - -
598S LEU* 3.8 8.3 - - - -
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Residues in contact with ASP 552 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551S THR* 1.3 73.1 - - - +
553S THR* 1.3 63.6 + - - +
555S PHE* 2.9 19.7 - - - +
556S VAL* 2.9 21.8 - - - +
579S THR* 5.2 2.2 - - - +
594S ALA 3.5 15.7 - - - +
595S SER* 3.8 8.7 - - - -
596S ALA* 3.0 24.9 + - - -
597S TRP* 2.8 21.5 + - - +
598S LEU* 3.1 22.3 + - - +
599S THR* 4.7 1.6 + - - -
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Residues in contact with THR 553 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551S THR* 2.6 17.1 + - - -
552S ASP* 1.3 72.0 - - - +
554S SER* 1.3 70.5 + - - -
555S PHE 2.7 1.6 + - - -
556S VAL 2.8 12.0 + - - -
557S GLU* 2.4 36.6 - - - +
576S LYS 4.0 5.2 - - - +
577S ASP 5.6 1.1 - - - +
579S THR* 3.2 29.6 + - + +
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Residues in contact with SER 554 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544S GLU* 3.1 15.3 + - - +
549S LYS 4.5 4.7 - - - -
550S ALA* 3.0 14.4 - - - -
551S THR* 2.3 48.2 + - - -
553S THR* 1.3 75.9 - - - +
555S PHE* 1.3 68.2 + - - +
557S GLU* 3.4 11.3 - - - +
558S LYS* 3.1 18.7 + - - +
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Residues in contact with PHE 555 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537S VAL* 3.8 12.1 - - + -
540S LEU* 3.7 8.5 - - + -
541S LEU* 3.2 63.9 - - + -
544S GLU* 4.0 17.9 - - + +
551S THR 2.6 11.2 + - - +
552S ASP* 2.9 19.7 - - - +
553S THR 2.7 1.4 + - - -
554S SER* 1.3 71.3 + - - +
556S VAL* 1.3 65.6 + - + +
558S LYS* 2.7 12.9 + - + +
559S LEU* 2.6 63.8 + - + -
581S PHE* 4.4 4.5 - + - -
594S ALA* 3.9 13.5 - - + -
597S TRP* 3.9 14.6 - + - -
598S LEU* 4.7 3.6 - - + -
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Residues in contact with VAL 556 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552S ASP 2.9 17.5 - - - +
553S THR 2.8 6.2 + - - +
555S PHE* 1.3 75.0 - - - +
557S GLU* 1.3 55.8 + - - +
559S LEU* 2.7 30.7 + - + +
560S ILE* 2.7 39.5 + - + +
576S LYS* 6.1 0.9 - - + -
579S THR* 3.7 27.6 - - + -
580S GLU 4.5 15.5 - - - +
581S PHE* 4.6 10.8 - - + -
594S ALA* 3.4 26.0 - - + -
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Residues in contact with GLU 557 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553S THR* 2.4 52.0 - - + +
554S SER* 3.4 12.1 - - - +
556S VAL* 1.3 73.8 - - - +
558S LYS* 1.3 61.1 + - - +
560S ILE* 3.0 23.6 - - - +
561S GLN* 3.0 10.0 + - - +
576S LYS* 4.8 7.7 - - - +
579S THR* 3.0 14.7 - - - +
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Residues in contact with LYS 558 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540S LEU* 4.9 13.2 - - + -
543S GLU* 4.0 18.5 + - - +
544S GLU* 3.5 32.4 + - + +
547S PHE* 6.0 2.8 - - - -
554S SER 3.1 8.3 + - - +
555S PHE* 2.7 16.5 + - + +
557S GLU* 1.3 72.1 - - - +
559S LEU* 1.3 56.4 + - - +
561S GLN* 2.5 73.1 + - + +
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Residues in contact with LEU 559 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537S VAL* 3.9 19.7 - - + -
540S LEU* 3.4 26.8 - - + +
555S PHE* 2.6 38.6 + - + +
556S VAL* 2.7 23.0 + - + +
558S LYS* 1.3 73.7 - - - +
560S ILE* 1.3 60.5 + - - +
562S GLU* 3.4 0.9 + - - +
563S GLN* 3.3 25.0 + - + +
564S GLY 3.8 2.4 + - - -
569S PHE* 3.7 15.5 - - + -
581S PHE* 3.2 51.1 - - + -
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Residues in contact with ILE 560 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556S VAL* 2.7 44.6 + - + +
557S GLU* 3.0 21.3 - - - +
559S LEU* 1.3 74.2 - - + +
561S GLN* 1.3 63.5 + - - +
564S GLY* 2.9 35.2 - - - +
569S PHE* 4.7 20.4 - - + -
571S LYS* 5.2 15.5 - - + -
580S GLU 5.8 1.1 - - - +
581S PHE* 5.6 0.4 - - + -
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Residues in contact with GLN 561 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540S LEU* 4.7 1.3 - - - +
557S GLU 3.0 7.2 + - - +
558S LYS* 2.5 68.7 + - + +
560S ILE* 1.3 75.0 - - - +
562S GLU* 1.3 106.4 + - - +
563S GLN 4.5 0.2 - - - -
564S GLY* 4.8 0.5 - - - -
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Residues in contact with GLU 562 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534S PRO* 5.1 2.4 - - - +
535S PRO* 3.7 36.3 - - + +
540S LEU* 4.0 12.6 - - + -
558S LYS 3.1 1.0 + - - -
559S LEU 4.1 2.7 - - - +
561S GLN* 1.3 118.2 + - - +
563S GLN* 1.3 89.5 + - - +
565S ASN* 5.4 0.3 + - - -
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Residues in contact with GLN 563 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527S LEU* 3.6 35.9 - - + +
534S PRO* 4.9 8.7 - - - +
535S PRO* 2.7 32.4 + - - +
536S GLY* 4.4 2.4 - - - -
537S VAL* 5.0 3.6 - - + -
540S LEU* 4.3 8.5 - - - +
559S LEU* 3.3 10.5 + - + +
562S GLU* 1.3 98.2 - - - +
564S GLY* 1.3 55.9 + - - +
565S ASN* 2.5 26.6 + - - -
566S HIS* 3.2 30.7 + - + +
569S PHE* 4.2 14.6 - - + -
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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
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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