Contacts of the strand formed by residues 128 - 134 (chain B) in PDB entry 3F7F
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 PHE 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ASN* 3.8 29.2 - - + -
121B VAL 4.1 1.1 - - - -
122B ILE* 3.4 33.7 - - + -
126B GLY 5.2 0.2 - - - +
127B SER* 1.3 73.9 - - - +
129B LEU* 1.3 62.1 + - - +
130B THR* 3.5 6.9 + - - -
151B HIS 3.6 5.4 - - - +
153B GLN* 2.7 29.7 + - - +
155B PRO* 3.8 19.3 - - + -
158B PHE* 5.9 4.3 - + + -
166B LEU* 3.9 17.0 - - + -
174B SER* 5.2 3.6 - - - -
186B LEU* 3.9 22.9 - - + -
194B TYR* 3.3 46.4 - + - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 4.0 17.3 - - + -
97B LEU* 3.8 29.4 - - + -
98B PRO* 4.6 0.4 - - + -
119B VAL 4.3 0.4 - - - -
120B ASN* 3.4 5.7 - - - +
121B VAL* 3.0 45.8 + - + +
123B LEU* 4.4 17.7 - - + -
127B SER 3.8 1.0 - - - -
128B PHE* 1.3 76.0 - - - +
130B THR* 1.3 71.3 + - - +
131B LEU* 4.2 9.9 - - + -
150B PHE* 3.8 34.3 - - + -
151B HIS 3.8 7.0 - - - +
152B LEU* 3.8 24.0 - - + +
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Residues in contact with THR 130 (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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118B LEU* 4.0 21.3 - - + -
119B VAL 3.4 1.6 - - - -
120B ASN* 3.2 20.0 + - - +
128B PHE* 3.5 8.8 + - - -
129B LEU* 1.3 81.4 + - - +
131B LEU* 1.3 61.4 + - - +
132B GLN* 4.9 4.9 - - + +
149B TRP 3.4 0.3 - - - +
150B PHE* 2.8 27.5 - - - -
151B HIS* 3.0 32.5 + - + +
153B GLN* 4.4 9.9 + - - -
191B GLY 6.2 0.2 - - - +
192B VAL* 5.2 4.1 + - + +
194B TYR* 4.5 10.3 - - + +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 4.3 8.1 - - + -
79B LEU* 4.4 6.3 - - + -
95B ILE* 3.6 36.3 - - + -
97B LEU* 4.9 6.3 - - + -
117B LEU 3.3 2.3 - - - +
118B LEU* 3.4 7.6 - - - +
119B VAL* 2.6 67.2 + - + +
121B VAL* 5.7 2.0 - - + -
129B LEU* 4.6 11.0 - - + -
130B THR* 1.3 73.9 - - - +
132B GLN* 1.3 62.4 + - - +
133B LEU* 4.0 5.6 - - + -
149B TRP* 3.0 35.0 - - + +
150B PHE* 3.6 17.9 - - + -
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Residues in contact with GLN 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLN* 3.0 30.4 + - - +
117B LEU 3.7 2.9 - - - -
118B LEU* 3.5 26.5 - - + +
130B THR* 4.9 4.7 - - + +
131B LEU* 1.3 73.1 - - - +
133B LEU* 1.3 62.1 + - - +
134B PRO* 3.5 8.4 - - - +
148B GLU 4.3 4.2 + - - +
149B TRP* 2.6 38.2 + - - +
151B HIS* 3.2 31.6 + - + -
191B GLY 4.7 11.9 + - - -
192B VAL* 5.1 2.4 - - - +
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Residues in contact with LEU 133 (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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26B LEU* 4.4 9.9 - - + -
81B PHE* 3.8 23.1 - - + -
93B ILE* 5.6 1.6 - - + -
95B ILE* 3.3 35.0 - - + -
116B GLN* 3.4 2.6 - - - -
117B LEU* 2.7 52.1 + - + +
119B VAL* 4.7 5.4 - - + -
131B LEU* 4.8 3.1 - - + -
132B GLN* 1.3 81.7 - - - +
134B PRO* 1.3 67.7 - - + +
135B LEU* 3.3 0.7 + - - -
137B PHE* 5.0 5.8 - - + -
138B LEU* 4.5 19.2 - - + +
145B LEU* 4.1 19.1 - - + -
149B TRP* 4.6 9.2 - - + -
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Residues in contact with PRO 134 (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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115B GLN 4.0 0.9 - - - +
116B GLN* 3.6 24.0 - - + +
132B GLN 3.5 9.0 - - - +
133B LEU* 1.3 82.1 - - + +
135B LEU* 1.3 69.3 + - - +
136B SER* 2.9 17.7 + - - +
137B PHE* 2.9 20.1 + - + +
138B LEU* 3.3 10.6 + - - +
145B LEU* 4.0 29.6 - - + -
146B ASN 5.8 1.6 - - - +
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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