Contacts of the helix formed by residues 589 - 602 (chain T) in PDB entry 5IJ7
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 PRO 589 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PRO* 3.6 31.2 - - + +
116B LEU* 4.6 4.9 - - - -
117B GLN* 4.7 5.2 - - + +
586T GLU* 3.7 17.4 - - + +
587T LYS 3.5 9.6 - - - +
588T ASP* 1.4 83.6 - - - +
590T GLU* 1.3 67.9 + - - +
591T TRP* 3.2 24.7 - - + +
592T LEU* 3.0 38.2 + - + +
593T ARG* 3.6 3.3 + - - -
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Residues in contact with GLU 590 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F ARG* 4.0 23.7 + - - -
282F PHE* 5.3 0.9 - - - -
588T ASP 3.3 2.8 + - - -
589T PRO* 1.3 69.0 - - - +
591T TRP* 1.4 60.9 + - - +
593T ARG* 2.9 58.1 + - + +
594T GLU* 3.1 30.4 + - - +
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Residues in contact with TRP 591 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B SER* 4.0 11.2 - - - -
115B PRO* 2.8 41.3 + - + +
116B LEU* 3.5 20.0 - - + -
120B PHE* 4.0 13.2 - + - -
680B LYS* 3.6 21.8 - - - -
218F VAL* 3.2 26.2 - - + -
281F HIS* 3.6 50.1 - + + +
282F PHE* 3.6 11.7 - - + -
589T PRO* 3.2 18.7 + - + +
590T GLU* 1.4 81.6 + - - +
592T LEU* 1.3 84.0 + - + +
594T GLU 3.9 0.2 - - - -
595T LYS* 2.9 30.2 + - + +
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Residues in contact with LEU 592 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.8 9.6 - - + -
117B GLN 5.5 2.5 - - - +
118B GLN 5.7 2.7 - - - +
120B PHE* 4.1 7.4 - - + -
295B PHE* 3.3 41.3 - - + -
588T ASP* 5.8 0.4 - - - -
589T PRO* 3.0 32.5 + - + +
591T TRP* 1.3 114.6 - - + +
593T ARG* 1.4 59.1 + - - +
595T LYS* 3.2 3.1 + - - +
596T THR* 2.9 31.0 + - - -
622T MET* 3.8 13.6 - - + +
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Residues in contact with ARG 593 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586T GLU* 5.9 1.2 - - - +
588T ASP* 2.8 53.3 + - - +
589T PRO 3.6 2.6 + - - -
590T GLU* 2.9 39.0 + - + +
592T LEU* 1.4 76.1 - - - +
594T GLU* 1.3 60.5 + - - +
596T THR* 3.2 19.2 - - - +
597T ILE* 3.3 16.6 + - - +
619T LEU* 3.6 25.6 - - + +
622T MET* 3.6 17.5 - - + -
623T LYS* 5.8 6.4 - - - +
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Residues in contact with GLU 594 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F PHE* 3.5 44.9 - - + +
590T GLU* 3.1 27.4 + - - +
591T TRP 3.6 3.4 - - - +
593T ARG* 1.3 76.2 - - - +
595T LYS* 1.3 56.5 + - - +
597T ILE* 3.3 16.2 - - + +
598T THR* 2.8 60.5 + - - -
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Residues in contact with LYS 595 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 4.1 19.7 - - + -
295B PHE* 3.9 9.6 - - + -
680B LYS* 6.0 0.9 - - - +
218F VAL* 4.6 9.4 - - + -
219F GLU* 4.4 17.4 + - - +
282F PHE* 3.9 20.6 - - + -
591T TRP* 2.9 32.0 + - + +
592T LEU* 3.2 8.7 + - - +
594T GLU* 1.3 73.4 - - - +
596T THR* 1.3 59.0 + - - +
598T THR* 3.7 8.4 - - + +
599T GLN* 2.8 68.1 + - - +
602T GLU* 5.5 3.0 + - - -
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Residues in contact with THR 596 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TYR 4.3 2.3 + - - -
293B ASP* 4.7 2.8 + - - -
295B PHE* 3.6 28.2 - - - -
592T LEU 2.9 8.5 + - - +
593T ARG* 3.2 19.3 - - - +
595T LYS* 1.3 75.1 - - - +
597T ILE* 1.4 63.8 + - + +
599T GLN* 3.3 3.8 + - - +
600T ILE* 2.9 35.8 + - + +
615T LYS* 5.9 0.7 - - - -
618T ASN* 3.0 35.0 + - + -
619T LEU* 4.4 4.0 - - + -
622T MET* 3.8 25.3 - - - -
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Residues in contact with ILE 597 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593T ARG 3.3 14.5 + - - +
594T GLU* 3.3 29.6 - - + +
596T THR* 1.4 77.6 - - + +
598T THR* 1.4 62.6 + - - +
601T GLU* 3.2 30.4 + - + +
615T LYS* 3.5 40.7 + - + +
619T LEU* 4.0 28.9 - - + -
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Residues in contact with THR 598 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F GLU* 6.2 1.3 - - + -
282F PHE* 4.7 17.5 - - + -
594T GLU* 2.8 39.8 + - - -
595T LYS* 3.9 9.9 - - + +
597T ILE* 1.4 79.2 - - - +
599T GLN* 1.3 60.7 + - + +
601T GLU* 4.1 5.4 + - - +
602T GLU* 3.5 30.8 + - - +
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Residues in contact with GLN 599 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B PHE* 4.6 1.7 - - - -
293B ASP* 2.9 27.8 + - - +
294B CYS 5.7 0.4 + - - -
295B PHE* 3.1 36.9 - - - -
595T LYS* 2.8 48.3 + - - +
596T THR* 3.7 4.7 - - - +
598T THR* 1.3 75.2 - - + +
600T ILE* 1.3 63.3 + - - +
601T GLU 3.2 1.3 - - - -
602T GLU* 3.2 26.3 + - - +
603T PHE* 3.3 17.8 - - - -
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Residues in contact with ILE 600 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LEU* 5.1 1.6 - - + -
292B TYR* 3.5 34.8 - - + +
293B ASP* 3.8 16.6 - - + +
596T THR* 2.9 27.4 + - + +
597T ILE 4.2 0.7 - - - +
599T GLN* 1.3 74.6 - - - +
601T GLU* 1.3 61.6 + - - +
603T PHE* 3.3 23.4 + - + +
606T VAL* 5.6 0.7 - - + -
611T LYS* 3.4 51.7 - - + +
614T MET* 4.2 13.5 - - + -
615T LYS* 3.9 20.6 - - + +
618T ASN* 4.1 6.5 - - - +
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Residues in contact with GLU 601 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597T ILE* 3.2 18.9 + - + +
598T THR* 4.2 7.0 - - - +
599T GLN 3.2 0.2 - - - -
600T ILE* 1.3 75.4 - - - +
602T GLU* 1.3 56.5 - - - +
603T PHE 3.2 2.5 - - - +
608T GLU* 2.9 25.1 - - - +
611T LYS* 3.0 32.3 + - - +
612T GLU* 5.1 0.2 - - - +
615T LYS* 2.8 30.2 + - - +
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Residues in contact with GLU 602 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595T LYS* 5.5 2.3 + - - -
598T THR* 3.5 26.6 + - - +
599T GLN* 3.2 24.2 + - + +
601T GLU* 1.3 75.0 - - - +
603T PHE* 1.3 61.9 + - + +
604T SER* 3.6 3.3 + - - -
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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