Contacts of the strand formed by residues 205 - 211 (chain H) in PDB entry 1AXS
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 THR 205 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H GLY* 4.2 13.5 - - - -
119H PRO* 3.6 19.3 - - + +
198H VAL 4.8 0.4 - - - -
199H ASN* 3.6 3.9 - - - +
200H HIS* 3.1 35.9 + - - +
203H SER* 2.5 30.6 + - - +
204H ASN* 1.3 77.4 - - - +
206H LYS* 1.3 66.6 + - - +
207H VAL* 5.2 6.7 - - + -
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Residues in contact with LYS 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198H VAL 3.8 1.8 - - - -
199H ASN* 2.9 39.0 - - - +
204H ASN 3.9 3.3 + - - +
205H THR* 1.3 79.5 - - - +
207H VAL* 1.3 59.6 + - - +
208H ASP* 3.6 8.3 - - - +
1005H CD 3.5 19.3 - - - -
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Residues in contact with VAL 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H PRO* 4.6 11.7 - - + +
121H VAL* 3.3 36.3 - - + -
196H CYS 4.1 1.1 - - - -
197H ASN* 3.4 3.3 - - - -
198H VAL* 3.0 38.0 + - + +
199H ASN* 4.1 1.7 - - - +
205H THR* 5.2 7.9 - - + -
206H LYS* 1.3 78.2 - - - +
208H ASP* 1.3 81.5 + - - +
209H LYS* 3.8 15.0 - - + +
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Residues in contact with ASP 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195H ILE* 3.6 18.4 - - + +
196H CYS 3.4 9.0 - - - -
197H ASN* 3.6 16.2 + - - +
206H LYS* 3.6 12.8 - - - +
207H VAL* 1.3 92.0 - - - +
209H LYS* 1.3 64.1 + - - +
210H LYS 3.7 0.5 + - - -
1005H CD 2.5 27.6 - - - -
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Residues in contact with LYS 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 4.3 23.8 - - + +
123H PRO* 3.7 25.4 - - + +
140H CYS* 4.3 8.8 - - - -
195H ILE* 3.2 1.1 - - - -
196H CYS* 2.9 37.0 + - - -
207H VAL* 3.8 13.8 - - + +
208H ASP* 1.3 74.5 - - - +
210H LYS* 1.3 85.9 + - - +
211H VAL* 4.4 0.5 - - - +
212H GLU* 5.6 2.4 + - - -
123L GLU* 2.7 31.1 + - - +
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Residues in contact with LYS 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H PRO* 4.3 1.9 - - - +
193H THR* 4.4 10.5 - - + -
194H TYR 3.3 9.4 - - - +
195H ILE* 3.3 18.5 - - + +
208H ASP 3.7 0.6 + - - -
209H LYS* 1.3 99.5 + - - +
211H VAL* 1.3 65.6 + - - +
212H GLU* 3.1 40.2 + - + +
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Residues in contact with VAL 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H PRO* 3.4 25.1 - - + -
124H LEU 3.8 5.8 - - - +
125H ALA* 3.7 26.0 - - + +
126H PRO* 3.9 8.0 - - + +
138H LEU* 3.7 25.0 - - + +
139H GLY 3.8 15.9 - - - +
140H CYS* 4.4 4.9 - - - -
154H TRP* 4.1 12.1 - - + -
193H THR* 3.3 17.2 - - - +
194H TYR* 3.1 16.5 + - - +
209H LYS 4.4 4.5 - - - +
210H LYS* 1.3 78.9 - - - +
212H GLU* 1.3 63.6 + - - +
213H PRO* 4.4 2.3 - - - +
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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