Contacts of the strand formed by residues 172 - 177 (chain I) in PDB entry 6PST
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 TYR 172 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158I ASP 3.8 3.8 - - - +
159I SER* 3.5 17.5 - - - -
170I VAL* 4.0 27.6 - - + +
171I LEU* 1.3 72.3 - - - +
173I ASN* 1.3 60.0 + - - +
187I GLU* 3.6 1.3 - - - -
188I PHE* 3.1 38.7 + + + +
432I LEU* 4.0 15.6 - - + +
435I ILE* 3.4 31.4 + - + -
436I ARG* 3.8 35.9 - - + -
442I VAL* 3.7 17.9 - - + -
70N LYS* 5.0 0.9 + - - -
71N HIS* 3.1 37.3 + + + -
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Residues in contact with ASN 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156I PHE 3.7 1.7 - - - +
157I PHE* 3.5 2.8 - - - +
158I ASP* 2.9 50.2 + - - +
159I SER* 4.5 4.2 - - - +
160I ASP* 4.9 1.4 - - - +
171I LEU 4.0 9.5 + - - -
172I TYR* 1.3 75.3 - - - +
174I ALA* 1.3 61.7 + - - +
175I ARG* 5.1 5.1 + - - +
185I ASP* 4.0 10.3 - - - +
186I PHE 3.0 14.1 - - - +
187I GLU* 3.6 16.4 + - + +
432I LEU* 3.9 4.5 - - - +
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Residues in contact with ALA 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I VAL* 4.7 1.3 - - + -
156I PHE 3.2 5.2 - - - +
157I PHE* 3.3 35.7 - - + -
173I ASN* 1.3 74.1 - - - +
175I ARG* 1.3 57.4 + - - +
185I ASP* 2.6 20.5 - - - +
186I PHE* 2.8 24.5 + - + -
428I VAL* 4.1 14.4 - - + -
432I LEU* 3.8 17.1 - - + +
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Residues in contact with ARG 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I GLY 3.4 2.6 - - - +
155I VAL* 3.2 3.2 - - - -
156I PHE* 2.9 39.2 + - + +
173I ASN* 5.3 5.8 - - - +
174I ALA* 1.3 74.4 - - - +
176I ILE* 1.3 61.8 + - - +
177I ILE* 3.3 36.8 + - + +
183I TRP* 4.1 31.4 - - + +
184I LEU 3.7 8.7 - - - +
185I ASP* 3.7 20.2 + - - +
200I ARG* 3.1 45.1 - - - +
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Residues in contact with ILE 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I GLY 3.5 8.7 - - - +
155I VAL* 4.4 2.7 - - + +
175I ARG* 1.3 72.8 - - - +
177I ILE* 1.3 61.5 + - - +
178I PRO* 3.4 8.8 - - - +
183I TRP* 3.9 1.2 - - - -
184I LEU* 2.9 59.0 + - + +
186I PHE* 4.1 11.9 - - + -
395I TYR* 3.5 20.0 + - - +
397I LEU* 4.7 6.7 - - + -
405I PHE* 4.1 22.0 - - + -
420I LEU* 4.0 17.0 - - + -
424I ASP 4.9 1.8 - - - +
425I ILE* 5.3 1.1 - - + -
428I VAL* 4.1 28.5 - - + -
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Residues in contact with ILE 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I ARG* 3.2 42.2 - - - +
152I SER 5.3 0.9 - - - +
153I PRO* 3.4 5.0 - - + +
154I GLY* 2.9 34.2 + - - +
156I PHE* 3.3 26.2 - - + -
175I ARG* 3.3 33.4 - - + +
176I ILE* 1.3 71.7 - - - +
178I PRO* 1.3 77.1 - - + +
183I TRP* 3.9 26.2 - - + +
397I LEU* 4.7 1.4 - - - +
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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