Contacts of the helix formed by residues 589 - 602 (chain I) in PDB entry 5LS6
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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G PRO* 4.0 22.7 - - + +
116G LEU* 5.0 2.0 - - + -
117G GLN* 4.1 28.5 - - + +
118G GLN* 5.8 2.5 - - - +
587I LYS* 4.3 12.3 - - + -
588I ASP* 1.4 92.9 - - - +
590I GLU* 1.3 66.0 + - - +
591I TRP* 3.2 23.9 + - + +
592I LEU* 3.3 29.5 + - + +
593I ARG* 3.7 2.8 + - - +
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Residues in contact with GLU 590 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H ARG* 3.2 34.5 + - - -
292H GLN* 4.9 2.9 + - - +
293H LYS* 3.4 18.6 + - - +
295H HIS* 4.4 11.1 + - + +
296H PHE* 6.1 0.9 - - - -
588I ASP 3.3 5.6 + - - -
589I PRO* 1.3 71.6 - - - +
591I TRP* 1.3 70.5 + - + +
593I ARG* 3.2 28.5 + - - +
594I GLU* 3.2 19.9 + - + +
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Residues in contact with TRP 591 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G SER* 4.1 4.7 - - - -
115G PRO* 2.9 30.1 + - + +
116G LEU* 3.7 22.9 - - + -
120G PHE* 3.5 32.8 - + - -
680G LYS* 4.0 17.3 - - + -
232H VAL* 3.3 28.3 - - + -
295H HIS* 3.8 41.3 - + + -
296H PHE* 3.6 16.6 - + + -
589I PRO* 3.8 14.7 - - + +
590I GLU* 1.3 86.4 - - + +
592I LEU* 1.3 82.0 + - + +
594I GLU* 3.2 5.8 + - - +
595I LYS* 2.8 43.0 + - + +
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Residues in contact with LEU 592 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 5.3 2.9 - - + -
118G GLN* 5.9 4.7 - - - +
120G PHE* 3.6 22.9 - - + -
295G PHE* 3.6 31.6 - - + -
588I ASP* 5.0 2.5 - - - +
589I PRO* 3.3 26.6 + - + +
590I GLU 3.2 0.8 - - - -
591I TRP* 1.3 112.0 - - + +
593I ARG* 1.3 60.8 + - - +
595I LYS* 3.2 12.0 + - - +
596I THR* 3.2 18.4 + - - -
622I MET* 3.7 21.5 - - + -
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Residues in contact with ARG 593 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588I ASP* 2.7 62.4 + - - +
589I PRO 3.7 2.4 + - - +
590I GLU* 3.2 20.0 + - - +
592I LEU* 1.3 78.6 - - - +
594I GLU* 1.3 62.8 + - + +
596I THR* 3.6 1.6 + - - -
597I ILE* 3.4 26.0 + - + +
619I LEU* 3.5 38.9 - - + +
622I MET* 4.3 10.3 - - - -
623I LYS* 5.1 15.9 - - - +
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Residues in contact with GLU 594 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H ARG* 5.4 10.6 + - - +
296H PHE* 3.4 32.8 - - + +
590I GLU* 3.2 15.9 + - + +
591I TRP* 3.2 9.8 + - - +
593I ARG* 1.3 78.1 - - - +
595I LYS* 1.3 63.0 + - - +
597I ILE* 2.9 25.0 + - - +
598I THR* 3.0 23.9 + - + +
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Residues in contact with LYS 595 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G PHE* 4.9 9.5 - - + -
295G PHE* 4.0 20.9 - - + -
232H VAL* 4.3 11.9 - - + -
233H GLU* 3.8 23.7 + - - -
296H PHE* 4.3 13.0 - - + -
591I TRP* 2.8 36.5 + - + +
592I LEU* 3.2 14.1 + - - +
594I GLU* 1.3 72.9 - - - +
596I THR* 1.3 56.9 + - - +
598I THR* 2.7 23.6 + - - +
599I GLN* 3.0 32.2 + - + +
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Residues in contact with THR 596 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G TYR 4.8 0.2 - - - +
293G ASP 5.4 1.3 - - - +
295G PHE* 3.2 18.1 - - + -
592I LEU 3.2 5.1 + - - -
593I ARG* 3.8 6.7 - - - -
594I GLU 3.2 0.4 - - - -
595I LYS* 1.3 75.2 - - - +
597I ILE* 1.3 60.7 + - + +
599I GLN* 2.7 7.1 + - - +
600I ILE* 2.7 51.1 + - + +
615I LYS* 5.2 2.9 - - - +
618I ASN* 3.1 39.5 - - + +
619I LEU* 5.4 2.7 - - + -
622I MET* 3.1 23.8 - - - +
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Residues in contact with ILE 597 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593I ARG* 3.4 16.5 + - + +
594I GLU* 2.9 17.3 + - - +
596I THR* 1.3 74.8 - - - +
598I THR* 1.3 63.8 + - + +
601I GLU* 3.2 28.1 + - + +
615I LYS* 3.5 35.6 - - + +
619I LEU* 3.8 31.4 - - + -
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Residues in contact with THR 598 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296H PHE* 5.6 10.0 - - + -
594I GLU* 3.0 21.4 + - + +
595I LYS* 2.7 32.8 + - - +
597I ILE* 1.3 79.1 - - + +
599I GLN* 1.3 51.5 + - - +
601I GLU* 3.0 10.3 + - - +
602I GLU* 2.7 42.3 + - - +
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Residues in contact with GLN 599 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G ASP* 3.1 42.4 + - + +
294G CYS 4.7 1.6 + - - +
295G PHE* 3.9 25.9 - - - -
595I LYS* 3.0 29.6 - - + +
596I THR* 2.7 9.4 + - - +
598I THR* 1.3 75.1 + - - +
600I ILE* 1.3 64.7 + - + +
602I GLU* 3.4 21.2 + - + +
603I PHE* 3.4 16.1 - - + -
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Residues in contact with ILE 600 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G LEU* 4.8 5.4 - - + -
292G TYR* 3.7 34.8 - - + +
293G ASP* 4.5 10.3 - - + +
596I THR* 2.7 37.9 + - + +
599I GLN* 1.3 74.2 - - + +
601I GLU* 1.3 60.0 + - - +
603I PHE* 3.3 25.1 + - + +
611I LYS* 3.6 47.3 - - + +
614I MET* 4.2 10.5 - - + -
615I LYS* 3.6 23.1 - - + -
618I ASN* 4.4 1.8 - - - +
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Residues in contact with GLU 601 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597I ILE* 3.2 20.6 + - + +
598I THR* 3.0 13.6 + - - +
600I ILE* 1.3 77.0 - - - +
602I GLU* 1.3 58.6 + - - +
603I PHE 3.1 8.8 + - - +
608I GLU 5.3 1.7 - - - +
611I LYS* 3.7 22.9 + - - +
612I GLU* 5.3 0.9 - - - +
615I LYS* 3.6 25.6 + - + +
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Residues in contact with GLU 602 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346H SER* 4.1 19.9 - - - -
598I THR* 2.7 27.7 + - - +
599I GLN* 3.4 21.5 - - + +
600I ILE 3.2 0.4 - - - -
601I GLU* 1.3 72.9 - - - +
603I PHE* 1.3 60.7 + - + +
604I SER* 3.3 3.6 + - - -
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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
------------------------------------------------------------
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