Contacts of the helix formed by residues 199 - 210 (chain J) in PDB entry 6AHU
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 GLY 199 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103H ARG* 4.8 6.6 - - - +
104H VAL 6.0 1.5 - - - +
28J LEU* 3.5 20.6 - - - +
30J TYR* 3.8 0.2 - - - -
198J ARG* 1.3 73.6 - - - +
200J PRO* 1.3 70.4 - - - +
201J TYR* 3.2 3.1 - - - -
202J ASP* 2.9 24.9 + - - +
203J VAL* 3.0 12.8 + - - +
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Residues in contact with PRO 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J PHE* 3.7 36.6 - - + -
5J ALA* 3.7 22.2 - - + -
28J LEU* 4.3 1.8 - - + -
29J GLY* 3.9 27.1 - - - +
30J TYR* 3.7 15.5 - - + +
199J GLY* 1.3 84.4 - - - +
201J TYR* 1.3 67.8 + - + +
202J ASP 3.2 0.4 + - - -
203J VAL* 3.6 18.5 + - + +
204J ALA* 3.6 13.7 + - - +
221J VAL* 4.8 8.5 - - + +
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Residues in contact with TYR 201 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H TRP* 4.6 15.8 - - - -
104H VAL* 5.8 7.6 - - + +
105H ILE 5.3 9.0 - - - -
119H ARG* 6.4 2.0 - - - -
4J PHE* 3.8 30.1 - + - -
199J GLY* 3.2 1.2 - - - -
200J PRO* 1.3 80.7 - - + +
202J ASP* 1.3 59.8 + - - +
204J ALA* 4.3 11.2 + - - +
205J ASN 4.8 0.7 + - - -
218J LYS* 5.7 3.8 - - + -
100L HIS* 4.1 21.4 + + - +
103L GLU* 3.2 18.6 + - + +
331L PHE* 3.4 43.0 - + - -
333L LYS* 4.9 13.1 - - + +
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Residues in contact with ASP 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H TRP* 3.7 28.6 - - - +
90H THR* 2.8 37.9 + - - +
102H PHE* 5.0 6.9 - - - +
103H ARG* 6.3 0.2 - - - -
104H VAL* 4.1 30.2 - - + +
198J ARG* 4.2 8.0 - - + +
199J GLY* 2.9 15.7 + - - +
201J TYR* 1.3 77.6 - - - +
203J VAL* 1.3 63.5 + - - +
204J ALA 3.3 2.0 + - - -
205J ASN* 3.5 13.3 + - - +
206J LEU* 3.9 6.8 + - - +
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Residues in contact with VAL 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H THR* 6.0 1.8 - - + -
7J LEU* 6.3 0.9 - - + -
30J TYR* 3.7 20.0 - - + +
156J TYR* 3.4 28.0 - - + +
187J ILE* 3.6 26.0 - - + +
188J SER* 5.9 0.7 - - - -
197J ILE* 5.8 1.1 - - + -
198J ARG* 4.1 11.7 - - + +
199J GLY 3.0 15.0 + - - +
200J PRO* 4.0 10.1 - - + +
201J TYR 3.6 0.4 - - - -
202J ASP* 1.3 78.1 - - - +
204J ALA* 1.3 56.6 + - - +
206J LEU* 2.9 24.6 + - - +
207J GLY 3.3 8.1 + - - -
221J VAL* 4.8 16.2 - - + -
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Residues in contact with ALA 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187J ILE* 5.2 1.3 - - - -
200J PRO 3.6 13.3 + - - +
201J TYR* 4.4 6.1 - - - +
202J ASP 3.3 1.0 - - - -
203J VAL* 1.3 77.5 - - - +
205J ASN* 1.3 56.2 + - - +
207J GLY 4.1 2.0 - - - +
208J LEU 3.4 13.5 + - - -
217J ALA* 3.4 34.9 - - - +
218J LYS* 4.0 14.8 - - + -
221J VAL* 5.4 4.7 - - + +
333L LYS* 3.5 27.4 + - + -
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Residues in contact with ASN 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H VAL* 3.3 49.7 - - - +
86H TRP* 3.2 46.1 - - + +
87H SER* 5.0 6.1 - - - -
201J TYR 4.8 1.0 + - - -
202J ASP 3.5 9.1 + - - +
203J VAL 3.2 1.0 - - - -
204J ALA* 1.3 75.7 - - - +
206J LEU* 1.3 55.1 + - - +
207J GLY 3.2 1.8 - - - -
208J LEU* 3.4 18.6 - - - +
209J LEU* 2.4 35.3 + - - +
333L LYS* 4.1 5.0 - - - +
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Residues in contact with LEU 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H SER* 5.8 3.6 - - - +
90H THR* 4.0 25.1 - - + +
91H LEU* 4.5 13.0 - - + -
156J TYR* 3.6 51.4 - - + -
187J ILE* 4.5 2.0 - - + -
202J ASP 3.9 5.1 + - - +
203J VAL* 2.9 14.7 + - - +
205J ASN* 1.3 77.7 - - - +
207J GLY* 1.3 58.3 + - - +
209J LEU* 3.4 20.2 - - + +
210J PHE* 3.1 53.1 + - + -
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Residues in contact with GLY 207 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J ILE* 3.5 17.9 - - - +
203J VAL 3.3 8.1 + - - -
204J ALA* 3.9 4.2 + - - -
205J ASN 3.2 0.2 - - - -
206J LEU* 1.3 78.9 - - - +
208J LEU* 1.3 57.1 + - - +
210J PHE* 3.3 14.6 - - - +
211J GLY 3.0 25.7 + - - +
212J LEU* 3.6 15.1 - - - +
217J ALA* 4.2 7.6 - - - -
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Residues in contact with LEU 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H VAL* 3.8 16.6 - - + -
204J ALA 3.4 10.6 + - - +
205J ASN* 3.0 26.6 + - - +
207J GLY* 1.3 73.8 - - - +
209J LEU* 1.3 61.4 + - - +
210J PHE 3.2 0.9 - - - -
211J GLY* 2.9 22.0 + - - +
213J SER 4.0 15.3 - - - +
214J GLU* 3.9 22.9 - - + +
217J ALA* 4.1 5.4 - - + +
6L ARG* 3.8 27.6 - - + +
7L LEU* 3.4 11.9 - - + +
333L LYS* 3.5 22.4 - - - +
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Residues in contact with LEU 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E PHE* 3.6 47.5 - - + -
51H LEU* 5.0 8.3 - - + -
52H PHE* 3.9 18.6 - - + -
83H VAL* 5.9 0.9 - - + -
87H SER* 3.3 30.3 - - - +
91H LEU* 6.0 2.9 - - + -
170J ILE* 3.9 18.6 - - + +
174J LEU* 4.7 2.3 - - - +
205J ASN* 2.4 29.7 + - - +
206J LEU* 3.4 22.9 - - + +
208J LEU* 1.3 70.5 - - - +
210J PHE* 1.3 62.5 + - + +
211J GLY 3.4 0.3 + - - -
7L LEU* 4.2 11.3 - - + +
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Residues in contact with PHE 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J LEU* 3.6 34.1 - - + -
156J TYR* 4.8 9.4 - - + -
169J THR* 4.0 16.6 - - - -
170J ILE* 3.6 26.0 - - + -
173J ALA* 3.6 24.9 - - + -
174J LEU* 3.4 19.2 - - - +
177J MET* 3.4 27.2 - - + +
187J ILE* 3.9 16.4 - - + -
206J LEU* 3.1 39.8 + - + -
207J GLY* 3.3 11.7 - - - +
208J LEU 3.2 0.2 - - - -
209J LEU* 1.3 78.5 - - + +
211J GLY* 1.3 55.8 + - - +
212J LEU* 3.6 4.9 + - + -
3L THR* 5.7 0.5 - - - +
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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