Contacts of the strand formed by residues 137 - 143 (chain I) in PDB entry 1FPY
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 ASP 137 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I PHE* 3.6 4.4 - - - +
136I ASP* 1.3 84.1 - - + +
138I ILE* 1.3 62.3 + - - +
139I ARG* 2.6 35.6 + - - +
150I ALA 4.6 1.6 - - - +
151I ILE* 3.7 1.4 - - - -
152I ASP* 2.9 48.5 + - + +
252I THR* 4.2 0.4 - - - +
164J TYR 5.0 2.1 + - - +
167J GLY* 3.5 13.0 - - - -
168J ASN* 2.6 38.4 + - - +
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Residues in contact with ILE 138 (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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462C PHE* 4.4 8.5 - - + -
466C TYR* 3.5 49.4 - - + +
135I PHE* 5.0 3.8 - - + -
137I ASP* 1.3 75.1 - - - +
139I ARG* 1.3 68.8 + - - +
140I PHE* 4.0 12.1 - - + -
149I VAL* 4.3 9.4 - - + -
150I ALA 3.4 16.4 - - - +
151I ILE* 4.0 21.8 - - + -
252I THR* 4.0 2.9 - - + +
160J SER 3.9 1.6 - - - +
168J ASN* 2.8 36.9 + - - +
169J LYS 3.9 2.5 - - - -
170J GLY* 3.8 20.1 - - - +
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Residues in contact with ARG 139 (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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137I ASP* 2.6 42.1 + - - +
138I ILE* 1.3 79.9 - - - +
140I PHE* 1.3 65.4 + - - +
148I HIS* 4.4 7.1 + - + +
149I VAL* 3.2 2.1 - - - +
150I ALA* 2.6 62.5 + - + +
152I ASP* 5.8 0.4 - - - +
160J SER 3.1 8.3 - - - +
161J SER* 3.6 14.5 + - - +
162J THR 3.4 21.1 - - - +
163J LYS* 3.5 42.7 - - - +
168J ASN* 3.7 7.2 - - + +
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Residues in contact with PHE 140 (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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459C PRO 4.5 3.4 - - - +
462C PHE* 3.6 36.8 - - + -
463C GLU* 3.4 35.2 - - + -
466C TYR* 4.4 9.9 - + + -
138I ILE* 4.0 22.2 - - + -
139I ARG* 1.3 80.8 - - - +
141I GLY* 1.3 63.8 + - - +
148I HIS* 3.0 27.9 + - - +
149I VAL* 3.9 6.1 - - + -
160J SER* 2.8 59.8 + - - -
161J SER* 3.2 2.3 + - - -
170J GLY* 4.8 14.8 - - - -
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Residues in contact with GLY 141 (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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459C PRO* 4.3 4.1 + - - +
463C GLU* 4.7 4.7 - - - -
140I PHE* 1.3 83.4 - - - +
142I ALA* 1.3 61.6 + - - -
147I SER* 3.0 4.6 - - - -
148I HIS* 2.8 44.8 + - - +
160J SER* 4.3 4.9 - - - -
161J SER* 4.8 2.9 - - - -
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Residues in contact with ALA 142 (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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460C VAL* 4.1 18.8 - - + +
463C GLU* 4.0 18.4 + - - +
141I GLY* 1.3 75.6 - - - +
143I SER* 1.3 63.0 + - - +
146I GLY 3.5 5.8 - - - +
147I SER* 3.8 12.8 - - - -
452I ARG* 4.6 6.9 + - - +
456I THR* 4.8 5.8 - - + +
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Residues in contact with SER 143 (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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158C TRP* 6.1 0.2 - - - +
261C PHE* 5.6 6.9 - - - +
142I ALA* 1.3 76.8 - - - +
144I ILE* 1.3 69.9 + - - +
145I SER* 3.0 22.7 + - - -
146I GLY 2.7 21.2 + - - +
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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