Contacts of the strand formed by residues 137 - 143 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135J PHE* 3.7 5.3 - - - +
136J ASP* 1.3 83.6 - - + +
138J ILE* 1.3 61.7 + - - +
139J ARG* 2.7 37.5 + - - -
150J ALA 4.7 1.2 - - - +
151J ILE* 3.7 1.4 - - - -
152J ASP* 2.9 47.8 + - + +
252J THR* 4.9 0.2 - - - -
164K TYR 5.1 0.9 + - - -
167K GLY* 3.4 10.5 - - - -
168K ASN* 2.5 39.2 + - - +
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Residues in contact with ILE 138 (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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462D PHE* 4.0 17.3 - - + -
466D TYR* 3.5 46.9 - - + +
135J PHE* 4.8 3.4 - - + -
137J ASP* 1.3 75.2 - - - +
139J ARG* 1.3 64.8 + - - +
140J PHE* 4.0 16.1 - - + -
149J VAL* 4.3 5.2 - - + -
150J ALA 3.6 3.8 - - - +
151J ILE* 3.8 29.2 - - + -
252J THR* 4.2 2.0 - - + +
160K SER 4.0 1.7 - - - +
168K ASN* 2.9 36.2 + - - +
169K LYS 3.5 16.8 - - - +
170K GLY* 3.7 8.2 - - - -
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Residues in contact with ARG 139 (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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137J ASP* 2.7 41.7 + - - -
138J ILE* 1.3 78.3 - - - +
140J PHE* 1.3 65.5 + - - +
148J HIS* 4.3 10.8 + - - +
149J VAL* 3.2 2.9 - - - +
150J ALA* 2.7 62.8 + - + +
152J ASP* 5.5 2.4 - - - +
160K SER 3.2 5.6 - - - +
161K SER* 3.8 13.2 + - - +
162K THR 3.4 25.8 - - - +
163K LYS* 3.7 41.8 - - - +
168K ASN* 3.7 6.1 - - + +
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Residues in contact with PHE 140 (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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459D PRO 4.4 3.1 - - - +
462D PHE* 3.6 37.9 - + + -
463D GLU* 3.4 35.7 - - + -
466D TYR* 4.3 9.9 - + + -
138J ILE* 4.0 23.6 - - + -
139J ARG* 1.3 79.1 - - - +
141J GLY* 1.3 62.6 + - - +
148J HIS* 3.1 25.5 + - - +
149J VAL* 4.0 5.8 - - + -
160K SER* 2.8 61.5 + - - -
161K SER* 3.2 2.9 + - - -
170K GLY* 4.7 15.3 - - - -
172K ARG* 6.2 1.3 - - + -
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Residues in contact with GLY 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D PRO* 4.2 4.6 + - - +
463D GLU* 4.2 11.7 - - - -
140J PHE* 1.3 78.4 - - - +
142J ALA* 1.3 62.2 + - - +
147J SER* 3.2 3.3 - - - -
148J HIS* 2.9 42.8 + - - +
160K SER* 4.3 3.1 - - - -
161K SER* 4.7 2.7 - - - -
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Residues in contact with ALA 142 (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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460D VAL* 3.9 28.5 - - + +
463D GLU* 4.0 19.3 + - - +
141J GLY* 1.3 73.8 - - - +
143J SER* 1.3 62.8 + - - +
146J GLY 3.4 9.2 - - - +
147J SER* 4.2 6.3 - - - -
452J ARG* 4.5 5.7 + - - +
456J THR* 4.9 5.6 - - + -
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Residues in contact with SER 143 (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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261D PHE* 5.5 7.0 + - - +
142J ALA* 1.3 75.5 - - - +
144J ILE* 1.3 67.9 + - - +
145J SER* 3.2 20.4 + - - -
146J GLY* 2.8 21.8 + - - +
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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