Contacts of the strand formed by residues 150 - 155 (chain B) in PDB entry 5FJV
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 PRO 150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A VAL* 5.2 0.7 - - + -
129A PHE* 3.7 35.8 - - + -
178A TRP* 3.3 43.0 - - + +
83B VAL 3.2 7.4 - - - +
84B TRP* 4.2 1.8 - - + -
131B VAL* 4.5 7.1 - - - +
132B THR 5.5 1.0 + - - -
133B HIS* 3.8 34.5 + - + +
135B THR* 4.4 1.3 - - + -
148B VAL 3.7 0.4 - - - -
149B PRO* 1.3 93.9 - - + +
151B ALA* 1.3 64.1 + - - +
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Residues in contact with ALA 151 (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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129A PHE* 4.1 3.4 - - - -
81B THR 3.5 0.3 - - - +
82B ASN* 3.2 6.6 - - - +
83B VAL* 2.5 46.1 + - + +
85B LEU* 5.5 1.8 - - + -
130B ALA 5.6 0.2 - - - +
131B VAL* 5.2 9.9 - - + -
132B THR 6.2 0.4 - - - +
149B PRO 4.9 1.8 - - - +
150B PRO* 1.3 77.7 - - - +
152B ILE* 1.3 64.6 + - - +
153B TYR* 3.2 37.7 - - + +
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Residues in contact with ILE 152 (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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125A ALA 3.2 24.7 - - - +
126A ASP* 3.9 20.9 - - + +
127A GLY 4.6 11.9 - - - +
129A PHE* 3.5 17.2 - - + -
70B ILE* 5.0 2.0 - - + -
80B THR* 4.5 15.7 - - + -
81B THR 3.3 4.7 - - - +
82B ASN* 3.0 41.1 - - + +
127B GLY* 5.9 0.3 - - - -
128B GLU* 5.3 7.8 + - - +
151B ALA* 1.3 75.3 - - - +
153B TYR* 1.3 66.2 + - - +
154B LYS* 4.0 12.1 + - - +
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Residues in contact with TYR 153 (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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79B MET 3.7 0.2 - - - +
80B THR* 3.2 5.5 - - - +
81B THR* 2.7 49.8 + - - +
83B VAL* 3.3 26.7 - - + -
85B LEU* 3.9 18.7 - - + +
119B ILE 5.2 0.5 + - - -
121B LEU* 3.8 28.9 + - + +
124B ASN* 5.4 0.2 - - - -
128B GLU 3.5 26.0 - - - +
130B ALA* 3.4 29.7 + - - -
131B VAL* 4.1 3.6 - - - +
151B ALA* 3.2 23.6 - - + -
152B ILE* 1.3 76.9 - - - +
154B LYS* 1.3 61.9 + - - +
155B SER* 4.0 1.1 - - - +
173B MET* 3.9 18.8 - - + -
175B PHE* 3.9 18.1 - + - -
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Residues in contact with LYS 154 (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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126A ASP 4.9 8.9 + - - -
154A LYS* 6.0 1.4 - - - +
78B MET* 4.1 26.6 - - + +
79B MET 3.3 4.9 - - - -
80B THR* 3.3 23.3 - - + +
121B LEU* 4.6 0.4 - - - +
124B ASN* 3.2 7.7 + - - +
125B ALA* 3.0 26.4 + - - +
126B ASP* 4.9 3.1 - - + +
127B GLY* 4.0 27.7 - - - +
128B GLU 5.2 0.4 - - - +
152B ILE* 4.0 17.0 + - - +
153B TYR* 1.3 73.9 - - - +
155B SER* 1.3 59.9 + - - +
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Residues in contact with SER 155 (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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78B MET* 4.1 1.1 - - - +
79B MET* 2.7 53.4 + - - +
81B THR* 4.5 3.1 + - - -
121B LEU* 3.6 18.8 - - - +
123B ASN* 2.9 24.9 - - - -
124B ASN 3.6 5.4 - - - -
125B ALA* 4.2 0.6 - - - +
153B TYR* 4.8 0.5 - - - +
154B LYS* 1.3 74.3 - - - +
156B SER* 1.3 60.2 + - - +
172B LYS 5.0 0.4 - - - -
173B MET* 4.0 17.0 - - - +
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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