Contacts of the strand formed by residues 89 - 97 (chain B) in PDB entry 1F5J
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 VAL 89 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B TRP* 3.1 12.8 - - - -
84B SER* 2.9 45.3 + - - +
87B PRO* 3.4 16.4 + - + +
88B LEU* 1.3 81.6 - - - +
90B GLU* 1.3 73.0 + - - +
91B PHE* 4.0 2.0 + - + +
137B PHE* 4.8 0.7 - - - -
138B ASP* 3.5 16.4 - - + +
140B TYR* 3.6 53.6 - - + +
168B ASN 4.2 0.9 - - - +
169B LEU* 3.9 7.4 - - + -
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Residues in contact with GLU 90 (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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45B LEU* 4.9 2.3 - - - +
81B TYR* 2.6 47.3 + - + +
82B GLY 3.5 4.7 - - - +
83B TRP* 3.4 22.3 - - + -
89B VAL* 1.3 73.1 - - - +
91B PHE* 1.3 58.8 + - - +
92B TYR* 4.0 10.1 + - + -
125B ARG* 4.6 3.1 + - - +
129B PRO 5.5 0.2 - - - +
137B PHE* 3.5 25.3 - - + -
138B ASP 3.2 4.9 + - - -
139B GLN* 2.7 60.6 + - + +
140B TYR 3.1 1.7 + - - -
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 5.2 3.4 - - + -
81B TYR* 3.4 11.8 - - - -
82B GLY* 2.9 57.0 + - - +
83B TRP* 3.3 28.3 - - - -
84B SER 4.2 0.2 - - - -
89B VAL* 4.2 4.7 - - + -
90B GLU* 1.3 74.6 - - - +
92B TYR* 1.3 69.9 + - - +
93B ILE* 5.6 2.0 - - + -
140B TYR* 3.3 14.6 - - + +
155B VAL* 5.0 4.0 - - + -
159B PHE* 3.7 25.1 - + - -
162B TRP* 3.6 26.2 - + + -
169B LEU* 4.0 17.3 - - + -
172B ILE* 4.2 14.8 - - + -
174B GLN 3.6 10.1 - - - -
175B ILE* 4.3 10.1 - - + -
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Residues in contact with TYR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 4.7 0.7 - - - +
77B TYR* 3.9 12.2 - + - -
79B CYS* 3.6 22.7 - - + -
80B ILE 3.4 4.9 - - - -
81B TYR* 3.7 22.3 - + - -
90B GLU* 4.0 19.3 + - + -
91B PHE* 1.3 80.9 - - - +
93B ILE* 1.3 63.3 + - - +
94B VAL* 3.9 4.7 - - + -
139B GLN* 3.7 20.1 + - - -
140B TYR 2.9 6.6 + - - -
141B TRP* 3.4 54.2 - + + -
142B SER 3.0 21.9 + - - -
162B TRP* 3.4 11.4 - - - -
180B GLU* 2.6 35.1 + - - -
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Residues in contact with ILE 93 (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 CYS* 3.2 4.1 - - - +
80B ILE* 2.9 44.1 + - + +
91B PHE* 5.6 2.0 - - + -
92B TYR* 1.3 77.8 - - - +
94B VAL* 1.3 60.6 + - - +
95B GLU* 3.5 16.3 + - - +
118B TYR* 4.1 3.1 - - + -
142B SER* 3.3 4.7 - - - -
153B VAL* 3.9 23.3 - - + -
155B VAL* 4.0 21.5 - - + -
158B HIS* 3.6 56.8 - - + +
159B PHE* 5.3 0.2 - - + -
162B TRP* 4.0 12.6 - - + -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 4.5 8.7 - - + -
78B LEU 4.1 1.8 - - - +
79B CYS* 3.8 10.5 - - + -
92B TYR* 4.1 9.2 - - + -
93B ILE* 1.3 69.9 - - - +
95B GLU* 1.3 61.8 + - - +
96B SER 3.3 24.0 - - - +
97B TRP* 3.9 16.6 - - + -
102B PRO* 4.1 17.9 - - + -
118B TYR* 4.0 1.0 - - - -
141B TRP* 3.9 33.0 - - + -
142B SER 2.8 12.2 + - - +
143B VAL* 4.0 11.4 - - + -
144B ARG* 3.0 28.8 + - - +
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Residues in contact with GLU 95 (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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66B TYR* 2.7 36.7 + - + +
78B LEU* 2.9 14.3 + - + +
79B CYS* 4.9 3.8 - - - -
80B ILE* 5.2 2.9 - - + -
93B ILE* 3.9 14.8 - - - +
94B VAL* 1.3 75.3 - - - +
96B SER* 1.3 60.7 + - - +
97B TRP* 4.2 2.1 - - - -
118B TYR* 2.6 36.7 + - - -
144B ARG* 4.0 5.4 - - - +
146B SER 3.8 5.0 - - - +
147B LYS* 3.3 6.1 - - - -
148B ARG* 2.7 61.8 + - - +
153B VAL* 3.7 13.9 - - + -
177B LEU* 6.3 0.9 - - + -
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Residues in contact with SER 96 (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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70B TYR* 3.4 26.5 - - - -
77B TYR* 3.6 0.2 - - - -
78B LEU* 2.9 29.3 + - - -
94B VAL* 3.3 8.7 - - - +
95B GLU* 1.3 79.1 - - - +
97B TRP* 1.3 79.4 + - - +
147B LYS* 3.4 23.5 - - - +
148B ARG 3.3 15.0 - - - -
149B THR* 4.2 5.2 - - - +
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Residues in contact with TRP 97 (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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70B TYR* 3.6 14.5 - - - -
72B PRO* 4.4 1.7 - - - +
76B SER 3.1 15.7 - - - +
77B TYR* 4.3 1.8 - - + -
94B VAL* 3.9 10.3 - - + -
95B GLU 4.2 6.7 - - - -
96B SER* 1.3 88.4 + - - +
98B GLY* 1.3 72.6 + - - +
99B ASN 5.1 1.0 - - - -
100B TRP* 3.4 28.2 - - - +
101B ARG* 3.6 38.6 - - + +
102B PRO* 4.2 7.6 - - + -
143B VAL* 4.4 3.6 - - + -
144B ARG* 3.2 32.1 - - + -
145B THR 4.0 3.1 - - - -
146B SER* 3.9 22.7 - - - -
147B LYS* 3.1 47.3 + - + +
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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