Contacts of the strand formed by residues 136 - 144 (chain C) in PDB entry 3FUV
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 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C PHE* 4.6 2.0 - + - -
105C TRP* 3.8 20.2 - + - -
108C VAL* 3.8 25.4 - - + -
111C GLY* 4.6 1.1 - - - -
112C SER* 3.1 28.9 - - - +
113C LEU 3.8 18.2 - - - -
114C LEU* 4.1 3.1 - - + -
130C LEU* 3.7 46.2 + - + +
133C THR* 3.8 15.7 - - - -
134C GLY 3.6 2.5 - - - +
135C ARG* 1.3 83.4 - - - +
137C ALA* 1.3 59.9 - - - +
138C ARG 4.2 3.1 - - - +
139C LEU* 3.6 28.7 - - + -
199C PRO* 3.3 30.0 - - + +
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C THR* 4.9 8.3 - - - +
111C GLY* 3.6 26.5 - - - +
112C SER 2.7 10.1 + - - +
113C LEU* 4.8 6.1 - - + -
136C PHE* 1.3 73.5 - - - +
138C ARG* 1.3 66.5 + - + +
198C THR* 3.7 15.2 - - - +
199C PRO* 3.5 15.3 - - - +
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Residues in contact with ARG 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A PRO* 5.6 0.2 - - - +
187A PRO* 4.0 27.3 + - - +
42C ALA 3.5 24.2 - - - -
43C ALA* 2.9 23.5 + - - +
44C ARG 3.9 6.9 + - - -
45C PRO* 3.0 35.8 + - - +
47C THR* 4.8 4.8 + - - -
112C SER 3.9 1.9 + - - +
113C LEU* 3.3 20.3 - - + +
114C LEU 3.1 22.2 + - - -
136C PHE 3.6 0.8 - - - -
137C ALA* 1.3 87.7 + - - +
139C LEU* 1.4 70.7 + - - +
140C VAL* 3.8 15.3 - - + -
196C ARG* 3.8 15.5 - - + +
197C LEU 3.6 5.8 - - - +
198C THR* 4.7 9.8 + - - +
199C PRO* 4.1 0.9 - - - -
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Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C LEU* 3.3 33.4 - - + -
127C VAL* 4.4 7.9 - - + -
130C LEU* 4.1 21.8 - - + -
131C LEU* 3.9 31.4 - - + +
136C PHE* 3.6 26.7 - - + -
138C ARG* 1.4 79.3 - - - +
140C VAL* 1.3 62.5 + - - +
141C PHE* 3.9 18.0 - - + -
195C VAL 3.7 0.5 - - - +
196C ARG* 3.0 5.4 - - - -
197C LEU* 2.7 55.4 + - + +
199C PRO* 4.8 4.5 - - + -
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Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ILE* 3.8 26.6 - - + +
42C ALA* 3.7 24.0 - - + +
43C ALA* 3.9 6.1 - - - +
114C LEU 2.9 11.1 + - - +
115C VAL* 3.0 32.7 - - + +
116C ALA 3.1 3.3 + - - -
138C ARG* 3.8 18.2 - - + -
139C LEU* 1.3 78.7 - - - +
141C PHE* 1.3 60.1 + - - +
194C LEU* 3.7 28.5 - - + -
195C VAL 3.3 4.9 - - - +
196C ARG* 4.0 10.8 - - + -
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Residues in contact with PHE 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C LEU* 4.2 9.0 - - + -
116C ALA 3.0 13.2 - - - +
118C LEU* 3.7 27.8 - - + -
127C VAL* 3.8 20.6 - - + -
139C LEU* 3.9 21.8 - - + -
140C VAL* 1.3 78.3 - - - +
142C LEU* 1.3 59.9 - - - +
143C VAL* 3.9 20.6 - - + -
151C MET* 3.6 35.7 - - + -
193C SER 3.6 1.0 - - - +
194C LEU* 3.5 7.4 - - - -
195C VAL* 2.8 53.7 + - + -
197C LEU* 3.8 24.9 - - + -
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Residues in contact with LEU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 4.1 14.4 - - + -
39C ILE* 3.7 25.1 - - + -
60C LEU* 5.7 0.9 - - + -
116C ALA 2.9 8.8 + - - +
117C ASN* 3.6 32.8 - - + +
118C LEU* 3.0 31.5 + - - +
141C PHE* 1.3 74.0 - - - +
143C VAL* 1.4 60.7 + - - +
179C LEU* 4.2 13.0 - - + -
184C PHE* 3.9 24.0 - - + -
192C SER* 4.9 1.8 - - - -
193C SER 3.6 2.7 - - - +
194C LEU* 3.1 44.2 - - + -
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Residues in contact with VAL 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 4.7 5.6 - - + +
123C ALA* 4.1 24.0 - - + -
141C PHE* 3.9 23.1 - - + -
142C LEU* 1.4 73.4 - - - +
144C GLN* 1.3 61.9 + - - +
147C VAL* 3.5 22.7 - - + -
148C ALA* 3.5 35.7 - - + +
151C MET* 4.8 1.8 - - + -
192C SER* 3.2 8.3 - - - -
193C SER 3.0 27.2 + - - +
195C VAL* 3.8 16.4 - - + -
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Residues in contact with GLN 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C TYR* 3.2 50.1 - - + +
143C VAL* 1.3 74.0 - - - +
145C LYS* 1.3 67.0 + - - +
146C GLU* 3.3 10.7 - - + +
147C VAL* 3.0 28.3 + - + +
148C ALA 3.1 9.4 + - - -
188C PRO* 5.1 5.5 - - + +
190C VAL* 3.4 41.2 - - + +
191C TRP 3.6 6.3 - - - +
192C SER* 4.3 5.1 + - - +
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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