Contacts of the helix formed by residues 3198 - 3213 (chain G) in PDB entry 5JPQ
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 LEU3198 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2942G ASN* 5.5 11.2 - - + -
3195G TRP* 3.1 15.0 + - + +
3197G HIS* 1.3 75.8 - - + +
3199G LEU* 1.3 64.8 + - - +
3200G PRO 3.2 2.2 - - - -
3201G GLU* 2.8 22.1 + - + +
3202G MET* 3.0 13.6 + - + +
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Residues in contact with LEU3199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3195G TRP 3.8 3.0 + - - +
3196G LEU* 3.0 18.7 + - - +
3198G LEU* 1.3 76.3 - - - +
3200G PRO* 1.3 62.2 - - - +
3202G MET* 3.2 6.8 + - - +
3203G LEU* 3.0 26.3 + - - +
3229G ILE* 6.1 5.2 - - + -
3233G LEU* 5.6 8.1 - - + -
3236G SER* 5.6 10.5 - - - -
3239G SER* 5.9 1.3 - - - -
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Residues in contact with PRO3200 (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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3196G LEU 4.6 0.2 - - - -
3197G HIS 4.0 9.2 - - - +
3198G LEU 3.2 0.6 - - - -
3199G LEU* 1.3 79.3 - - - +
3201G GLU* 1.3 60.5 + - - +
3203G LEU* 4.1 3.7 - - + +
3204G PRO* 3.5 20.3 - - - +
3239G SER* 5.5 10.3 - - - -
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Residues in contact with GLU3201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2954G LEU* 6.3 2.9 - - + -
3197G HIS 4.8 1.2 + - - +
3198G LEU* 2.8 19.2 + - + +
3200G PRO* 1.3 71.5 - - - +
3202G MET* 1.3 57.2 + - - +
3204G PRO* 3.3 5.0 - - - +
3205G TYR* 2.7 33.2 + - - +
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Residues in contact with MET3202 (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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3127G GLN* 5.7 9.6 - - + -
3198G LEU* 3.0 13.9 + - + +
3199G LEU* 3.7 9.9 - - - +
3201G GLU* 1.3 77.1 - - - +
3203G LEU* 1.3 63.8 + - - +
3205G TYR* 2.9 18.4 + - - +
3206G ILE* 2.9 13.0 + - - +
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Residues in contact with LEU3203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3199G LEU 3.0 15.7 + - - +
3200G PRO* 4.8 2.0 - - + +
3202G MET* 1.3 75.5 - - - +
3204G PRO* 1.3 58.6 - - - +
3206G ILE* 2.9 10.6 + - + +
3207G SER* 2.7 26.2 + - - -
3239G SER* 4.9 21.5 - - - +
3240G MET* 5.6 3.8 - - - +
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Residues in contact with PRO3204 (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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3200G PRO 3.5 18.3 - - - +
3201G GLU* 3.3 5.5 - - - +
3202G MET 3.3 0.6 - - - -
3203G LEU* 1.3 76.9 - - - +
3205G TYR* 1.3 63.9 + - - +
3207G SER* 3.6 10.4 - - - -
3208G GLU* 3.2 20.8 + - - +
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Residues in contact with TYR3205 (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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2977G LEU* 5.0 20.0 - - + +
3201G GLU 2.7 17.4 + - - +
3202G MET* 2.9 14.8 + - - +
3204G PRO* 1.3 72.3 - - - +
3206G ILE* 1.3 63.2 + - - +
3208G GLU* 3.3 8.0 + - - +
3209G LEU* 3.2 18.9 + - - +
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Residues in contact with ILE3206 (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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3202G MET 2.9 11.2 + - - +
3203G LEU* 2.9 12.8 + - - +
3205G TYR* 1.3 78.7 - - - +
3207G SER* 1.3 62.9 + - - +
3209G LEU* 3.0 11.0 + - - +
3210G GLN* 2.9 20.3 + - - +
3221G ASN* 4.8 18.4 - - + +
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Residues in contact with SER3207 (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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3203G LEU 2.7 16.7 + - - -
3204G PRO* 3.6 13.9 - - - -
3205G TYR 3.2 0.2 - - - -
3206G ILE* 1.3 72.6 - - - +
3208G GLU* 1.3 57.2 + - - +
3210G GLN* 2.9 27.5 + - - +
3211G ASP* 3.5 5.4 + - - +
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Residues in contact with GLU3208 (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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3204G PRO 3.2 9.6 + - - +
3205G TYR* 3.7 9.4 - - - +
3206G ILE 3.3 0.2 - - - -
3207G SER* 1.3 75.5 - - - +
3209G LEU* 1.3 68.5 + - - +
3211G ASP* 3.2 15.2 + - - +
3212G ASP* 3.5 9.2 + - - +
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Residues in contact with LEU3209 (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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3205G TYR 3.2 9.4 + - - +
3206G ILE* 3.0 14.9 + - - +
3208G GLU* 1.3 78.9 - - - +
3210G GLN* 1.3 64.6 + - - +
3212G ASP* 2.9 25.6 + - - +
3213G ASP 4.0 2.3 + - - -
3217G VAL* 5.9 7.2 - - + -
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Residues in contact with GLN3210 (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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3206G ILE 2.9 10.6 + - - +
3207G SER* 2.9 18.6 + - - +
3209G LEU* 1.3 77.3 - - - +
3211G ASP* 1.3 59.5 + - - +
3212G ASP 3.3 0.2 + - - -
3213G ASP* 4.0 6.4 + - - -
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Residues in contact with ASP3211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3207G SER 3.5 4.7 + - - +
3208G GLU* 3.2 9.9 + - - +
3209G LEU 3.2 0.6 - - - -
3210G GLN* 1.3 79.3 - - - +
3212G ASP* 1.3 61.2 + - - +
3213G ASP* 3.5 5.1 + - - +
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Residues in contact with ASP3212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3208G GLU 3.5 6.3 + - - +
3209G LEU* 2.9 21.8 + - - +
3211G ASP* 1.3 73.7 - - - +
3213G ASP* 1.3 70.3 + - - +
3214G ASP* 4.7 10.1 - - + +
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Residues in contact with ASP3213 (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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3209G LEU 4.0 1.8 + - - -
3210G GLN 4.0 7.1 + - - -
3211G ASP 3.5 6.8 + - - +
3212G ASP* 1.3 80.2 - - - +
3214G ASP* 1.4 60.1 + - - +
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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