Contacts of the strand formed by residues 119 - 127 (chain B) in PDB entry 5FQD
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 THR 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B THR* 4.2 11.2 + - - +
73B HIS* 4.6 10.3 - - + -
81B ILE* 3.4 16.9 - - + +
82B PRO* 3.9 2.4 - - - +
113B LEU* 3.3 18.0 - - - +
117B ASP* 3.1 36.7 + - - +
118B ARG* 1.3 76.1 - - - +
120B PHE* 1.3 62.1 + - - +
138B THR* 3.7 33.2 - - + +
139B ALA 3.3 8.5 - - - +
140B GLU* 3.9 13.5 - - + +
162B ARG* 6.1 0.4 - - + -
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ILE* 3.5 4.9 - - - -
82B PRO* 3.4 14.6 - - + +
84B LEU* 3.7 30.1 - - + +
87B VAL* 5.0 2.0 - - + -
97B LEU* 4.5 5.4 - - + -
99B LEU* 3.9 20.2 - - + -
109B MET* 4.4 5.6 - - + -
110B VAL* 5.9 0.7 - - + -
113B LEU* 3.8 24.9 - - + -
119B THR* 1.3 73.4 - - - +
121B ALA* 1.3 62.0 + - - +
122B VAL* 3.6 26.7 - - + -
138B THR* 3.4 5.9 - - - -
139B ALA* 2.8 50.9 + - + -
141B ILE* 3.6 26.5 - - + -
157B VAL* 4.8 1.6 - - + -
159B ALA* 3.7 18.6 - - + -
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ILE* 3.5 19.9 - - + +
82B PRO 2.7 16.3 + - - +
83B VAL* 3.6 36.2 - - + +
84B LEU 4.2 1.4 + - - -
120B PHE* 1.3 77.2 - - - +
122B VAL* 1.3 63.3 + - - +
123B LEU* 3.9 1.1 - - + -
137B THR 4.0 2.9 - - - -
138B THR* 4.6 0.2 - - - +
165B PHE* 3.7 24.9 - - + -
180B ALA* 4.4 6.1 - - + -
182B VAL* 5.1 0.4 - - + -
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 5.7 0.2 - - - -
87B VAL* 3.9 19.3 - - + -
89B MET* 3.2 26.2 - - + +
90B ILE* 5.8 0.2 - - - -
91B LEU* 3.9 28.7 + - + +
97B LEU* 4.3 7.0 - - + -
120B PHE* 3.6 30.3 - - + -
121B ALA* 1.3 70.1 - - - +
123B LEU* 1.3 63.6 + - - +
124B ALA 3.6 0.2 + - - -
136B GLY* 3.3 2.5 - - - -
137B THR* 2.9 38.7 + - - +
139B ALA* 3.7 16.4 - - + -
165B PHE* 4.2 0.4 - - - -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 4.0 29.2 - - + +
87B VAL 5.4 0.5 + - - +
89B MET 3.6 15.0 - - - +
121B ALA* 4.0 0.8 + - + -
122B VAL* 1.3 71.8 - - - +
124B ALA* 1.4 58.9 + - - +
125B TYR* 3.3 55.2 + - + +
133B ALA* 3.8 9.2 - - + -
135B PHE 4.0 1.6 - - - -
165B PHE* 4.0 26.0 - - + -
167B VAL* 4.0 16.8 - - + -
170B LEU* 3.9 34.3 - - + -
178B GLN* 4.2 4.9 - - - +
180B ALA* 4.6 2.2 - - + -
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ILE* 3.8 33.4 - - + +
122B VAL 3.6 3.0 + - - +
123B LEU* 1.4 67.9 - - - +
125B TYR* 1.3 62.2 + - - +
126B SER* 3.5 3.3 + - - -
133B ALA* 3.5 14.9 - - - +
134B GLN* 4.3 2.6 + - - +
135B PHE* 3.1 27.7 + - + +
136B GLY* 4.2 0.9 - - - +
296B ILE* 3.9 20.6 - - + +
299B LEU* 4.0 11.2 - - + -
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 4.1 7.6 - - - +
84B LEU 5.2 0.2 + - - -
85B PRO* 5.2 2.9 + - - +
87B VAL 3.7 23.1 + - - -
88B MET* 4.0 30.6 + - - +
90B ILE* 4.6 8.4 - - - +
123B LEU* 3.3 54.1 + - + +
124B ALA* 1.3 70.5 - - - +
126B SER* 1.4 62.1 + - - +
128B VAL* 3.9 24.6 + - + +
131B ARG* 3.8 45.3 + - + -
132B GLU 3.3 16.6 - - - +
133B ALA* 4.1 2.9 - - + -
178B GLN* 4.0 9.7 + - - -
292B ASP* 4.9 6.1 - - - +
296B ILE* 3.5 11.4 - - - +
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ALA 3.5 4.8 + - - -
125B TYR* 1.4 72.4 - - - +
127B ASN* 1.4 63.5 + - - +
128B VAL* 4.0 1.0 + - - +
132B GLU* 3.1 17.2 + - - +
134B GLN* 2.8 41.6 + - - -
296B ILE* 4.0 13.7 - - - -
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Residues in contact with ASN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B TYR* 4.2 0.7 - - - -
126B SER* 1.4 79.2 + - - +
128B VAL* 1.3 61.4 + - - +
129B GLN* 3.3 21.9 + - - +
130B GLU* 3.1 30.1 + - - +
131B ARG* 3.3 2.3 + - - -
132B GLU* 2.8 67.3 + - - +
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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