Contacts of the strand formed by residues 144 - 154 (chain F) in PDB entry 6RI7
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 GLY 144 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140F ASN* 3.9 3.6 - - - -
141F THR* 2.5 56.2 + - - +
142F PRO 3.3 1.0 - - - -
143F ALA* 1.3 74.3 - - - +
145F GLU* 1.3 60.6 + - - -
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Residues in contact with GLU 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F VAL* 5.9 3.9 - - + +
139F VAL 2.9 15.5 - - - +
140F ASN* 3.8 8.5 - - + +
144F GLY* 1.3 75.9 - - - -
146F ALA* 1.3 68.6 + - - +
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Residues in contact with ALA 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F VAL* 3.1 6.7 - - - +
139F VAL* 2.9 33.5 + - + +
141F THR* 5.7 4.0 - - + +
144F GLY 5.3 0.4 - - - +
145F GLU* 1.3 80.6 - - - +
147F SER* 1.3 63.4 + - - +
148F TRP* 4.0 25.8 - - + -
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Residues in contact with SER 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F ASN* 4.2 9.9 - - - +
96F ASP* 5.0 9.4 + - - -
136F LEU* 5.4 4.0 - - - -
137F ALA 2.9 14.6 - - - -
138F VAL* 3.6 14.1 - - - -
146F ALA* 1.3 78.9 - - - +
148F TRP* 1.3 83.7 + - - +
149F TYR* 5.7 4.3 - - - -
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Residues in contact with TRP 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670D SER* 4.3 20.4 - - - -
93F ILE* 3.3 41.3 - - + +
94F GLU 3.0 27.6 - - - +
95F ASN* 3.6 23.0 - - - +
99F VAL* 4.8 6.2 + - - +
124F MET* 3.6 34.1 - - + -
135F ASP 3.7 0.2 - - - +
136F LEU* 3.6 0.9 - - - -
137F ALA* 2.9 41.4 + - + +
139F VAL* 3.9 22.9 - - + -
141F THR* 5.8 1.3 - - + -
146F ALA* 4.0 21.5 - - + -
147F SER* 1.3 93.4 - - - +
149F TYR* 1.3 73.2 + - - +
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Residues in contact with TYR 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F ILE* 3.2 7.4 - - - -
94F GLU* 2.9 42.5 + - + +
96F ASP* 5.4 8.3 + - - -
134F GLY* 6.1 1.6 - - - -
135F ASP 3.7 10.8 - - - +
136F LEU* 3.3 37.2 - - + +
147F SER* 5.7 4.3 - - - -
148F TRP* 1.3 83.1 - - - +
150F VAL* 1.3 70.4 + - - +
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Residues in contact with VAL 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F VAL* 5.7 2.9 - - + -
91F VAL* 5.0 4.3 - - + -
92F GLU 3.9 5.8 - - - +
93F ILE* 4.5 4.0 - - + -
128F LEU* 4.8 15.9 - - + -
131F LYS* 4.7 11.9 - - + -
132F GLU 3.2 24.7 - - - +
133F VAL* 3.0 25.7 + - - +
134F GLY* 4.8 1.2 - - - -
135F ASP* 3.6 18.6 + - + +
137F ALA* 5.5 4.0 - - + -
149F TYR* 1.3 80.4 - - - +
151F ASN* 1.3 65.8 + - - +
152F ALA 4.0 4.7 - - - +
153F ILE* 3.5 27.6 - - + -
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Residues in contact with ASN 151 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92F GLU* 2.9 30.6 + - + +
94F GLU* 2.5 44.3 + - + +
133F VAL* 4.4 4.7 - - - -
149F TYR 4.7 0.2 - - - +
150F VAL* 1.3 77.9 - - - +
152F ALA* 1.3 63.4 + - - +
153F ILE* 5.2 0.7 - - - -
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Residues in contact with ALA 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F TRP 4.0 3.1 - - - +
91F VAL* 3.3 24.5 - - - +
92F GLU* 3.4 34.6 + - + +
150F VAL* 4.0 2.2 - - - +
151F ASN* 1.3 81.9 - - - +
153F ILE* 1.3 73.2 + - - +
154F GLU* 5.4 8.7 - - + +
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Residues in contact with ILE 153 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82F GLU* 4.5 17.3 - - + +
83F GLY* 4.8 6.7 - - - +
84F LYS 4.7 1.8 - - - +
85F VAL* 3.7 29.4 - - + -
89F ALA* 4.6 4.9 - - + -
90F TRP 3.4 3.6 - - - -
91F VAL* 4.9 1.3 - - + -
132F GLU 4.4 2.0 - - - -
133F VAL* 3.7 32.1 - - + +
150F VAL* 3.5 24.2 - - + -
152F ALA* 1.3 83.8 - - - +
154F GLU* 1.3 70.9 + - - +
155F TYR* 4.3 28.0 - - + +
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Residues in contact with GLU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F GLU* 5.5 2.5 - - - -
89F ALA* 3.6 0.3 - - - -
90F TRP* 2.9 44.2 + - + +
102F ARG* 3.5 25.1 + - - -
152F ALA* 5.4 7.7 - - + +
153F ILE* 1.3 84.7 - - - +
155F TYR* 1.3 76.3 + - - +
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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