Contacts of the strand formed by residues 120 - 127 (chain B) in PDB entry 1F15
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 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B SER* 1.3 77.4 - - - +
121B VAL* 1.3 66.8 + - - +
122B TRP* 5.4 2.7 - - - -
152B VAL* 5.9 2.0 - - - -
153B TYR 3.4 4.9 - - - -
154B GLN* 3.1 47.1 - - + +
189B SER* 3.7 2.4 + - - -
190B LYS* 3.0 42.8 + - + +
191B ASP* 2.9 31.5 + - - +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 4.9 1.3 - - + -
117B PHE* 4.9 1.6 - - + -
119B SER* 4.8 1.3 - - - -
120B THR* 1.3 83.4 - - - +
122B TRP* 1.3 66.2 + - - +
123B VAL* 3.8 16.8 - - + -
151B LEU 4.1 0.2 - - - +
152B VAL* 3.5 6.4 - - - +
153B TYR* 2.9 47.5 + - + +
187B VAL* 4.2 14.4 - - + -
188B TYR 3.4 9.0 - - - +
189B SER* 4.8 4.9 - - - -
194B LEU* 3.7 30.1 - - + -
199B LEU* 4.3 20.2 - - + -
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Residues in contact with TRP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 5.0 1.3 - - - -
121B VAL* 1.3 85.1 - - - +
123B VAL* 1.3 64.7 + - - +
143B PHE* 3.7 53.3 - + + -
150B VAL* 4.5 10.1 - - + -
151B LEU 3.5 5.4 - - - +
152B VAL* 3.7 27.6 - - + +
186B LEU 3.7 0.7 - - - +
187B VAL* 3.6 2.1 - - - -
188B TYR* 3.1 42.1 + + + +
190B LYS* 3.7 43.6 - - + +
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 3.9 28.3 - - + -
111B VAL* 4.3 15.7 - - + -
121B VAL* 3.8 23.8 - - + +
122B TRP* 1.3 80.9 - - - +
124B THR* 1.3 72.5 + - - +
143B PHE* 4.1 1.7 - - - -
149B PRO 3.4 0.7 - - - +
150B VAL* 3.4 6.6 - - - +
151B LEU* 3.1 43.1 + - + -
166B LEU* 4.0 5.6 - - + +
185B VAL* 4.4 6.3 - - + -
186B LEU 3.5 13.0 - - - +
187B VAL* 4.3 11.9 - - + -
201B LEU* 5.2 1.1 - - + -
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 5.0 0.4 - - - -
123B VAL* 1.3 78.3 + - - +
125B VAL* 1.3 73.3 + - - +
126B ARG* 4.5 7.6 - - - +
142B MET* 4.9 3.5 + - - +
143B PHE* 3.3 24.3 - - - -
148B SER* 3.1 34.1 - - - +
149B PRO 2.9 23.3 + - - +
150B VAL* 4.3 2.3 - - + +
166B LEU* 4.1 5.2 - - - -
184B ALA 4.0 0.2 - - - +
185B VAL* 3.6 6.2 - - - +
186B LEU* 3.2 37.3 + - - +
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Residues in contact with VAL 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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90B LEU* 4.6 4.0 - - + -
107B LEU* 4.0 21.8 - - + +
109B ILE* 3.5 39.9 - - + -
124B THR* 1.3 75.1 - - - +
126B ARG* 1.3 62.2 + - - +
148B SER* 3.2 10.4 + - - -
149B PRO* 5.3 0.2 - - + -
166B LEU* 4.1 6.3 - - + -
168B TYR* 2.8 57.5 - - + -
183B TYR* 5.5 0.2 - - + -
184B ALA 3.5 9.2 - - - +
185B VAL* 3.7 15.7 - - + -
186B LEU* 5.8 0.2 - - - -
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Residues in contact with ARG 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 THR* 4.5 4.0 - - + +
125B VAL* 1.3 78.1 - - - +
127B LYS* 1.3 77.3 + - + +
128B VAL* 3.2 8.3 + - + +
142B MET* 2.7 73.1 + - + +
145B ASP* 2.6 30.1 + - - -
147B ALA* 3.2 11.7 - - - +
148B SER* 2.9 41.9 + - - +
168B TYR* 4.4 6.3 - - - +
183B TYR* 4.0 6.6 - - - -
184B ALA 2.9 30.4 + - - +
186B LEU* 4.9 5.4 - - + -
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Residues in contact with LYS 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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126B ARG* 1.3 78.9 - - + +
128B VAL* 1.3 64.1 + - - +
129B PRO* 3.3 11.8 - - + +
142B MET* 5.0 1.7 - - - +
168B TYR* 5.0 3.1 + - - +
173B MET* 5.2 17.4 + - - +
175B ALA* 5.8 2.8 - - - +
179B ASP* 5.4 5.4 + - - +
182B LYS* 3.7 31.4 - - + +
183B TYR* 3.6 47.9 + - + +
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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