Contacts of the helix formed by residues 554 - 563 (chain C) in PDB entry 6GYS
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 554 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229B PRO* 4.8 2.6 - - + +
266B ASN* 3.8 12.8 - - + +
267B PHE* 3.6 27.7 + - + -
83C ARG* 3.5 30.2 + - - -
307C ARG* 3.0 53.0 + - - +
551C LYS 4.8 2.8 - - - +
552C ASN* 3.6 4.4 + - - +
553C ASP* 1.3 79.0 + - - +
555C MET* 1.3 59.6 + - - +
556C PHE 3.2 2.5 - - - -
557C SER* 2.3 38.7 + - - +
558C LEU 2.8 10.6 + - - -
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Residues in contact with MET 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B PHE* 4.5 4.6 - - + -
269B VAL* 3.8 31.2 - - + -
282B GLU* 3.0 40.4 - - + +
285B ALA* 4.8 2.9 - - - -
286B LYS* 4.6 18.2 - - + -
289B LEU* 4.9 4.3 - - + -
553C ASP* 2.8 26.3 + - - +
554C GLU* 1.3 77.2 - - - +
556C PHE* 1.3 57.8 + - + +
558C LEU* 3.0 34.4 + - + +
559C ILE* 2.9 32.4 + - + +
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Residues in contact with PHE 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLU* 5.6 9.4 - - - -
550C LEU* 3.6 40.2 - - + -
551C LYS* 6.4 1.1 - - + -
553C ASP* 3.9 29.6 - - + +
554C GLU 3.2 0.6 - - - -
555C MET* 1.3 78.7 - - + +
557C SER* 1.3 56.3 + - - +
559C ILE* 3.3 15.4 + - + +
560C LYS* 2.9 43.3 + - - +
567C PRO* 5.0 11.8 - - + +
568C LEU 6.2 1.6 - - - -
569C ASN 5.1 17.3 - - - -
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Residues in contact with SER 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B PRO 5.2 3.6 + - - -
230B ASP* 5.0 2.4 - - - +
267B PHE* 4.3 3.8 - - - -
83C ARG* 4.7 11.6 + - - -
85C LEU* 5.5 6.7 - - - +
553C ASP 5.2 1.0 + - - -
554C GLU* 2.3 47.5 + - - +
556C PHE* 1.3 78.4 - - - +
558C LEU* 1.3 57.8 + - - +
560C LYS* 3.4 14.8 + - - +
561C GLY* 2.8 24.1 + - - -
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Residues in contact with LEU 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B ILE* 4.2 18.8 - - + +
267B PHE* 3.6 39.5 - - + -
285B ALA* 3.8 17.3 - - + +
289B LEU* 3.9 34.5 - - + -
554C GLU 2.8 7.0 + - - +
555C MET* 3.0 30.3 + - + +
557C SER* 1.3 75.9 + - - +
559C ILE* 1.3 60.5 + - - +
561C GLY* 3.0 2.4 + - - -
562C LEU* 2.9 52.3 + - + +
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Residues in contact with ILE 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B ASP* 5.3 3.1 - - - +
281B VAL* 4.5 6.1 - - + -
282B GLU* 3.8 38.4 - - + +
285B ALA* 4.1 18.2 - - + -
555C MET* 2.9 24.2 + - + +
556C PHE* 3.8 14.1 - - + +
558C LEU* 1.3 77.0 - - + +
560C LYS* 1.3 62.8 + - - +
562C LEU* 3.3 15.7 + - - +
563C GLY 3.5 3.3 + - - -
565C LEU* 2.9 49.4 - - + +
566C VAL 4.1 12.3 - - - +
567C PRO* 4.3 7.9 - - + -
568C LEU* 5.8 1.3 - - + -
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Residues in contact with LYS 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ASP* 4.0 14.3 - - - +
159B TRP* 4.5 0.3 - - - -
82C GLN* 5.9 0.8 + - - -
83C ARG 5.6 2.8 + - - -
84C ASP* 4.7 18.1 + - - +
85C LEU* 5.6 8.3 - - + -
556C PHE* 2.9 26.6 + - - +
557C SER* 3.5 16.1 - - - +
558C LEU 3.2 0.2 - - - -
559C ILE* 1.3 76.8 - - - +
561C GLY* 1.3 59.2 + - - +
563C GLY* 3.2 15.7 + - - +
565C LEU 4.8 1.6 - - - -
567C PRO* 4.0 32.1 - - + -
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Residues in contact with GLY 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B TRP* 3.2 17.8 - - - -
230B ASP* 3.9 11.7 - - - -
231B ILE* 4.5 2.9 - - - -
232B ARG* 3.2 35.4 + - - +
235B GLN* 5.1 0.2 - - - +
85C LEU* 5.5 1.3 - - - +
557C SER 2.8 18.6 + - - -
558C LEU 3.0 5.5 + - - -
560C LYS* 1.3 72.4 - - - +
562C LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ILE* 6.1 0.2 - - + -
135B GLU* 3.2 17.0 - - - +
159B TRP* 3.8 3.9 - - - -
231B ILE* 4.6 6.7 - - + -
235B GLN* 3.6 27.8 - - - +
285B ALA* 3.8 16.8 - - + +
288B THR* 4.7 17.3 - - + -
292B ILE* 5.0 3.6 - - + -
558C LEU* 2.9 38.4 + - + +
559C ILE* 3.7 10.3 - - - +
560C LYS 3.2 0.6 - - - -
561C GLY* 1.3 76.1 - - - +
563C GLY* 1.3 59.4 + - - +
564C SER 3.3 2.8 + - - -
565C LEU* 3.7 32.6 + - + +
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Residues in contact with GLY 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ARG* 3.5 19.1 - - - -
159B TRP* 3.6 11.0 - - - -
559C ILE 3.5 2.4 + - - +
560C LYS* 3.2 14.0 + - - +
561C GLY 3.2 0.8 - - - -
562C LEU* 1.3 75.8 - - - +
564C SER* 1.3 62.7 + - - -
565C LEU 3.1 11.9 + - - +
566C VAL* 4.1 3.3 + - - -
567C PRO* 5.5 0.9 - - - +
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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