Contacts of the helix formed by residues 596 - 604 (chain D) in PDB entry 6T8G
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 GLU 596 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644C ALA 5.2 1.6 - - - +
645C ASN* 4.6 6.8 + - - -
472D LYS* 2.4 35.5 + - - -
498D ASP* 5.1 1.8 - - - +
499D PRO* 3.4 22.1 - - + +
500D LYS* 4.0 30.9 + - + -
594D VAL 3.5 0.2 + - - -
595D ASP* 1.3 88.7 + - - +
597D PHE* 1.3 61.2 + - - +
598D ALA* 3.1 29.1 + - - +
599D ASP* 3.8 12.4 + - + +
600D MET* 4.0 0.2 - - - +
629D ALA* 3.3 14.4 + - - +
630D THR* 4.4 0.2 - - - -
631D GLN* 3.1 26.4 + - - +
632D ARG* 4.9 1.4 + - - +
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Residues in contact with PHE 597 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463D LEU* 4.5 13.0 - - + -
594D VAL* 3.7 17.7 - - + -
595D ASP 3.6 1.2 - - - -
596D GLU* 1.3 73.9 - - - +
598D ALA* 1.3 58.7 + - - +
599D ASP 3.4 0.9 - - - -
600D MET* 3.5 15.7 - - + -
601D MET* 2.9 53.5 + - + +
608D VAL* 6.4 0.4 - - + -
612D ILE* 5.7 8.1 - - + -
628D LEU* 3.6 37.0 - - + -
629D ALA 3.1 33.6 + - - -
630D THR* 4.4 11.2 - - + -
637D VAL* 3.9 13.7 - - + -
638D ILE* 5.1 4.0 - - + -
642D ILE* 3.9 28.9 - - + -
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Residues in contact with ALA 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644C ALA 6.1 0.4 - - - +
596D GLU* 3.1 23.6 - - - +
597D PHE* 1.3 79.5 - - - +
599D ASP* 1.3 60.3 + - - +
601D MET* 3.4 3.6 + - - +
602D MET 2.9 21.8 + - - -
629D ALA 4.5 1.0 + - - -
630D THR* 4.2 6.0 + - - +
632D ARG* 3.1 46.3 + - + +
637D VAL* 4.0 17.2 - - + +
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Residues in contact with ASP 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C ALA* 4.9 2.8 - - - +
617C GLN* 3.5 37.5 - - - +
644C ALA* 4.6 8.3 - - - +
645C ASN* 3.0 36.9 + - - +
499D PRO* 4.1 13.7 - - + +
500D LYS* 4.0 11.1 - - - -
521D MET* 5.3 1.2 - - - +
596D GLU* 3.8 8.2 + - - +
597D PHE 3.4 0.2 - - - -
598D ALA* 1.3 76.5 - - - +
600D MET* 1.3 61.4 + - - +
602D MET* 4.2 7.7 - - - +
603D ILE* 2.9 36.5 + - + +
632D ARG* 4.7 1.6 + - - -
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Residues in contact with MET 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497D ILE* 4.1 11.2 - - + -
499D PRO* 3.7 28.9 - - + -
521D MET* 3.7 28.5 - - + +
524D ALA* 3.8 25.6 - - + -
525D ALA 4.8 0.7 - - - +
528D LEU* 4.6 11.2 - - + -
594D VAL* 4.2 11.7 - - + -
596D GLU 4.0 0.2 - - - +
597D PHE* 3.2 23.3 + - + +
598D ALA 3.2 0.6 - - - -
599D ASP* 1.3 79.5 - - - +
601D MET* 1.3 57.9 + - + +
604D VAL* 2.9 29.5 + - + +
608D VAL* 4.2 31.2 - - + +
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Residues in contact with MET 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597D PHE* 2.9 39.6 + - + +
598D ALA* 3.7 4.7 - - - +
600D MET* 1.3 77.2 - - + +
602D MET* 1.3 59.4 + - - +
604D VAL 3.3 10.8 - - - +
605D GLY* 4.5 10.7 - - - +
606D LYS* 6.3 0.2 - - - -
608D VAL* 4.9 5.8 - - + -
609D GLU* 3.5 47.8 - - + +
612D ILE* 6.1 1.1 - - + -
632D ARG* 5.5 0.2 - - - -
636D ASP 4.7 5.6 - - - +
637D VAL* 3.2 35.9 - - + +
639D THR* 3.9 6.7 - - + +
642D ILE* 3.9 10.1 - - + -
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Residues in contact with MET 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609C GLU 4.4 0.7 - - - +
610C GLU* 4.1 31.1 - - + +
613C ALA* 3.6 32.8 - - + -
641C LEU* 3.7 48.9 - - + -
644C ALA* 5.4 1.1 - - + -
598D ALA 2.9 16.8 + - - +
599D ASP* 4.1 8.7 - - - +
600D MET 3.2 0.4 - - - -
601D MET* 1.3 80.5 - - - +
603D ILE* 1.3 80.2 + - + +
604D VAL 4.2 1.4 - - - +
605D GLY* 5.4 0.9 - - - -
632D ARG* 3.4 14.8 - - - +
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Residues in contact with ILE 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610C GLU* 4.8 3.3 - - + +
613C ALA 4.7 2.0 - - - +
614C ARG* 4.2 33.2 - - + +
617C GLN* 3.4 26.0 - - + +
521D MET* 3.7 34.3 - - + -
599D ASP* 2.9 24.8 + - + +
602D MET* 1.3 94.8 - - - +
604D VAL* 1.3 63.7 + - + +
605D GLY 4.0 1.2 + - - -
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Residues in contact with VAL 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D MET* 3.7 34.8 - - + +
522D LYS* 5.0 7.4 - - + +
525D ALA* 5.2 6.7 - - + -
600D MET* 2.9 21.1 + - + +
601D MET 3.3 10.6 - - - +
602D MET 4.5 0.4 - - - -
603D ILE* 1.3 80.3 - - + +
605D GLY* 1.3 69.8 + - - +
607D LYS* 5.5 6.3 - - + -
608D VAL* 3.7 26.7 - - + +
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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