Contacts of the strand formed by residues 138 - 147 (chain B) in PDB entry 1F11
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 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PRO* 4.1 20.0 - - + -
129B ALA* 6.3 0.9 - - + -
130B ALA* 3.9 25.1 - - + +
133B GLN* 5.3 2.9 - - + -
136B SER 3.8 7.2 - - - +
137B MET* 1.3 80.2 - - - +
139B THR* 1.3 72.4 + - - +
140B LEU* 4.0 11.8 + - + -
191B VAL 3.8 0.7 - - - +
192B THR* 3.5 1.3 - - - -
193B VAL* 2.6 49.3 + - + +
195B SER* 4.6 11.4 - - - -
200B ARG* 4.1 15.7 - - - +
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Residues in contact with THR 139 (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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114A THR* 5.4 6.1 - - - +
116A SER* 3.9 26.5 + - - +
118A PHE* 3.2 23.9 - - + -
135A PHE* 4.4 4.0 - - + -
137A ASN* 4.6 8.6 + - - +
126B PRO* 4.1 4.7 - - - +
138B VAL* 1.3 75.2 - - - +
140B LEU* 1.3 79.2 + - - +
190B SER* 4.2 15.0 - - - -
191B VAL 3.5 7.6 - - - +
192B THR* 3.2 21.8 + - - +
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Residues in contact with LEU 140 (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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118A PHE* 4.2 2.0 - - - -
124B LEU 3.8 3.8 - - - +
126B PRO* 3.4 34.5 - - + -
138B VAL* 4.1 7.0 - - + +
139B THR* 1.3 79.7 - - - +
141B GLY* 1.3 59.8 + - - +
157B TRP* 4.3 4.7 - - + -
190B SER* 3.2 5.7 - - - -
191B VAL* 2.8 44.6 + - + +
193B VAL* 4.5 8.1 - - + -
200B ARG* 3.4 38.6 - - + +
206B VAL* 3.6 26.7 - - + -
223B ILE* 3.7 20.0 - - + -
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Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 4.0 1.6 - - - -
135A PHE* 3.7 13.0 - - - -
124B LEU* 2.7 50.7 + - - +
140B LEU* 1.3 76.3 - - - +
142B CYS* 1.3 58.8 + - - +
157B TRP* 3.8 4.5 - - - -
189B SER 3.3 10.1 - - - -
223B ILE* 3.7 9.0 - - - +
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Residues in contact with CYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 4.0 18.2 - - - -
122B TYR 3.7 5.8 - - - -
123B PRO* 4.6 1.8 - - - -
124B LEU* 4.2 3.7 - - - +
141B GLY* 1.3 76.3 - - - -
143B LEU* 1.3 61.5 + - - +
144B VAL* 3.8 3.7 + - + +
154B VAL* 4.9 5.1 - - + +
157B TRP* 3.9 8.5 - - + -
188B SER* 3.4 3.5 - - - -
189B SER 2.8 33.4 + - - +
208B CYS* 2.0 53.6 - - + -
210B VAL* 4.9 0.4 - - - -
221B LYS* 4.7 2.9 - - - -
223B ILE* 4.6 7.2 - - - -
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Residues in contact with LEU 143 (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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124A GLN* 4.9 1.1 - - - +
131A SER* 4.0 22.7 - - - +
133A VAL* 4.4 15.7 - - + -
178A THR* 5.0 8.1 - - + +
120B SER 3.3 3.3 - - - +
121B VAL* 3.5 1.7 - - - +
122B TYR* 2.8 56.8 + - + +
124B LEU* 4.2 16.7 - - + +
142B CYS* 1.3 72.5 - - - +
144B VAL* 1.3 59.9 + - - +
145B LYS* 3.9 28.7 - - + -
186B THR* 4.1 14.6 - - + -
187B LEU 3.5 17.7 - - - +
188B SER* 3.8 13.7 - - - -
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Residues in contact with VAL 144 (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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119B PRO* 3.4 31.9 - - + -
120B SER 3.7 3.6 - - - +
121B VAL* 4.5 4.9 - - + -
142B CYS* 3.8 6.7 + - + +
143B LEU* 1.3 73.9 - - - +
145B LYS* 1.3 60.4 + - - +
147B TYR* 4.0 14.4 - - + -
152B VAL* 4.6 7.4 - - + -
154B VAL* 4.2 13.2 - - + -
186B THR* 3.5 1.9 - - - +
187B LEU* 2.8 46.2 + - + +
210B VAL* 3.2 39.7 - - + -
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Residues in contact with LYS 145 (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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124A GLN* 4.1 11.2 - - - +
131A SER* 4.1 11.4 - - - +
180A THR* 5.0 10.6 - - - +
119B PRO* 4.6 0.9 - - - -
120B SER* 2.9 42.1 + - - -
122B TYR* 3.9 25.8 - - + -
143B LEU* 3.8 20.6 - - + -
144B VAL* 1.3 73.4 - - - +
146B GLY* 1.3 64.0 + - - +
147B TYR* 3.7 2.2 - - - -
179B GLN* 3.7 28.6 + - - +
185B TYR 4.0 1.1 - - - -
186B THR* 3.2 22.0 - - + -
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Residues in contact with GLY 146 (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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117B THR* 3.6 13.5 - - - +
118B PRO 3.3 14.3 - - - +
120B SER* 5.4 0.7 + - - -
145B LYS* 1.3 78.7 - - - +
147B TYR* 1.3 57.5 + - - -
179B GLN* 3.9 15.4 - - - +
184B LEU* 3.9 20.0 - - - +
185B TYR 2.8 13.7 + - - -
186B THR* 3.4 3.2 + - - -
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Residues in contact with TYR 147 (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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117B THR 3.4 9.9 - - - +
119B PRO* 3.5 25.1 - - + -
144B VAL* 4.0 23.3 - - + -
146B GLY* 1.3 76.1 - - - +
148B PHE* 1.3 69.0 + - - +
149B PRO 3.6 17.9 - - - -
150B GLU* 3.0 25.8 + - - -
152B VAL* 3.0 30.9 - - + +
176B ALA* 3.2 17.2 - - - +
184B LEU* 3.6 2.8 - - - -
185B TYR* 2.7 73.2 + + + +
186B THR* 3.9 7.4 - - - -
187B LEU* 3.4 5.2 - - + +
212B HIS* 3.7 9.6 - + - +
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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