Contacts of the strand formed by residues 137 - 143 (chain A) in PDB entry 1F1H
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A PHE* 3.7 4.9 - - - +
136A ASP* 1.3 83.6 - - + +
138A ILE* 1.3 61.6 + - - +
139A ARG* 2.7 38.2 + - - -
150A ALA 4.7 1.2 - - - +
151A ILE* 3.7 1.6 - - - -
152A ASP* 2.9 48.3 + - + +
252A THR* 4.8 0.2 - - - -
164F TYR 5.0 1.4 + - - -
167F GLY* 3.3 10.6 - - - -
168F ASN* 2.6 39.3 + - - +
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 4.8 3.6 - - + -
137A ASP* 1.3 76.6 - - - +
139A ARG* 1.3 64.8 + - - +
140A PHE* 4.0 16.6 - - + -
149A VAL* 4.3 5.4 - - + -
150A ALA 3.6 3.6 - - - +
151A ILE* 3.8 27.6 - - + -
252A THR* 4.2 1.3 - - + +
160F SER 4.1 1.2 - - - +
168F ASN* 2.9 38.6 + - - +
169F LYS 3.6 15.3 - - - +
170F GLY* 3.8 5.6 - - - -
462G PHE* 4.0 17.7 - - + -
466G TYR* 3.5 49.8 - - + +
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Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASP* 2.7 42.1 + - - -
138A ILE* 1.3 79.4 - - - +
140A PHE* 1.3 64.2 + - - +
148A HIS* 4.3 10.0 + - - +
149A VAL* 3.2 2.6 - - - +
150A ALA* 2.7 63.3 + - + +
152A ASP* 5.5 2.2 - - - +
160F SER 3.3 4.7 - - - +
161F SER* 3.8 13.2 + - - +
162F THR 3.3 25.8 - - - +
163F LYS* 3.5 43.6 - - - +
168F ASN* 3.7 5.8 - - + +
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ILE* 4.0 23.6 - - + -
139A ARG* 1.3 80.2 - - - +
141A GLY* 1.3 61.8 + - - +
148A HIS* 3.1 24.1 + - - +
149A VAL* 4.0 5.6 - - + -
160F SER* 2.8 61.1 + - - -
161F SER* 3.1 3.1 + - - -
170F GLY* 4.7 16.8 - - - -
172F ARG* 6.3 0.9 - - + -
459G PRO 4.4 3.1 - - - +
462G PHE* 3.6 37.2 - - + -
463G GLU* 3.4 36.8 - - + -
466G TYR* 4.3 9.6 - + + -
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Residues in contact with GLY 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PHE* 1.3 79.4 - - - +
142A ALA* 1.3 62.2 + - - +
147A SER* 3.2 3.7 - - - -
148A HIS* 2.9 42.8 + - - +
160F SER* 4.3 3.1 - - - -
161F SER* 4.5 3.1 - - - -
459G PRO* 4.3 4.4 + - - +
463G GLU* 4.1 11.7 - - - -
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLY* 1.3 76.3 - - - +
143A SER* 1.3 61.5 + - - +
146A GLY 3.4 10.1 - - - +
147A SER* 4.2 6.7 - - - -
452A ARG* 4.4 6.5 + - - +
456A THR* 4.9 5.8 - - + -
460G VAL* 4.0 27.1 - - + +
463G GLU* 3.9 18.8 + - - +
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ALA* 1.3 74.9 - - - +
144A ILE* 1.3 67.5 + - - +
145A SER* 3.2 20.8 + - - -
146A GLY 2.8 23.0 + - - +
261G PHE* 5.6 6.8 + - - +
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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