Contacts of the helix formed by residues 550 - 558 (chain G) in PDB entry 4E2I
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 LYS 550 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117 GLU* 4.2 10.6 + - - +
147 ILE* 4.7 6.9 - - - +
397 GLU* 4.7 10.5 - - + -
396G CYS 3.6 1.4 + - - -
397G LEU 2.8 33.8 + - - +
398G LEU* 4.0 6.4 - - - +
399G PRO* 4.7 6.1 - - - +
430G SER* 5.4 0.8 + - - +
548G ARG* 2.7 38.1 + - + +
549G PRO* 1.3 73.4 - - - +
551G ASP* 1.3 62.7 + - - +
552G TYR* 3.0 44.7 + - + +
553G LEU* 3.6 27.5 + - + +
554G LYS* 3.6 15.4 + - - +
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Residues in contact with ASP 551 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377 ASN* 5.2 7.3 + - - +
397 GLU* 3.1 38.4 - - + +
407 GLY* 5.2 1.5 + - - +
549G PRO 4.7 4.0 - - - +
550G LYS* 1.3 69.5 - - - +
552G TYR* 1.3 58.3 + - - +
553G LEU 3.0 5.6 - - - -
554G LYS* 2.8 30.7 + - + +
555G HIS* 3.0 34.0 + - + +
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Residues in contact with TYR 552 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117 GLU* 3.0 36.4 + - - -
147 ILE* 3.9 6.6 - - + +
157 PHE* 5.1 2.5 - + - -
397 GLU* 4.5 21.9 + - + +
396G CYS* 2.7 25.0 + - + -
550G LYS* 3.0 40.0 + - + +
551G ASP* 1.3 79.0 - - - +
553G LEU* 1.3 74.5 + - + +
555G HIS* 4.1 8.7 - - - -
556G CYS* 3.1 26.7 + - - +
619G VAL* 3.1 43.7 - - + +
620G ALA* 3.8 18.2 - - - +
621G MET 4.8 1.6 - - - +
622G GLY* 3.9 6.6 - - - -
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Residues in contact with LEU 553 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393G TRP* 3.2 47.1 + - + +
396G CYS 3.4 23.3 - - - +
397G LEU* 3.7 27.1 - - + -
430G SER 4.5 6.1 - - - +
548G ARG 4.9 0.4 - - - +
550G LYS* 3.6 39.9 + - + +
551G ASP 3.0 0.4 - - - -
552G TYR* 1.3 93.6 - - + +
554G LYS* 1.3 65.7 + - - +
556G CYS* 3.2 14.9 - - - +
557G LEU* 3.2 9.5 + - - +
619G VAL* 4.1 2.7 - - + -
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Residues in contact with LYS 554 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550G LYS 3.6 6.8 + - - +
551G ASP* 2.8 18.0 + - - +
553G LEU* 1.3 77.5 - - - +
555G HIS* 1.3 82.0 + - + +
556G CYS 3.1 1.0 + - - -
557G LEU* 3.2 16.5 + - - +
558G GLU* 3.1 34.8 + - + +
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Residues in contact with HIS 555 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551G ASP* 3.0 39.5 + - + +
552G TYR* 4.1 3.8 - - - -
554G LYS* 1.3 93.4 - - + +
556G CYS* 1.3 62.5 + - - +
558G GLU* 2.9 45.4 + - - +
559G ARG* 3.3 8.5 + - - +
621G MET 5.5 1.6 - - - -
622G GLY* 2.8 36.4 - - - +
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Residues in contact with CYS 556 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393G TRP* 3.4 22.0 - - + -
552G TYR 3.1 21.0 + - - +
553G LEU* 3.2 9.6 - - - +
554G LYS 3.0 0.2 - - - -
555G HIS* 1.3 78.1 - - - +
557G LEU* 1.3 63.4 + - - +
558G GLU 3.1 0.2 - - - -
559G ARG* 3.2 8.7 + - - -
560G SER* 3.2 22.2 + - - -
619G VAL* 4.0 13.9 - - + -
622G GLY 3.8 1.5 + - - -
623G ILE 3.8 19.1 - - - +
625G VAL* 3.4 33.2 - - - -
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Residues in contact with LEU 557 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393G TRP* 3.7 36.3 - - + +
553G LEU 3.6 10.8 - - - +
554G LYS* 3.2 9.5 + - - +
556G CYS* 1.3 74.9 - - - +
558G GLU* 1.3 55.8 + - - +
559G ARG 3.0 5.4 - - - -
560G SER* 3.2 11.7 + - - +
561G GLU* 2.8 21.1 - - - +
563G LEU* 3.6 38.6 - - + -
564G LEU* 4.1 37.4 - - + +
569G ILE* 4.3 6.3 - - + -
419L LYS* 6.5 0.4 - - - -
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Residues in contact with GLU 558 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554G LYS* 3.1 31.5 - - + +
555G HIS* 2.9 43.2 + - - +
556G CYS 3.1 0.4 - - - -
557G LEU* 1.3 76.9 - - - +
559G ARG* 1.3 69.3 + - - +
561G GLU* 3.3 14.5 - - - +
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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