Contacts of the strand formed by residues 131 - 139 (chain F) in PDB entry 3A2C
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 ARG 131 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ARG* 5.4 3.1 - - - +
181A ASN* 5.7 2.0 + - - -
215A THR* 5.9 5.3 - - - +
273B PRO* 4.6 19.9 + - + +
276B LYS* 5.4 8.5 - - - +
277B THR* 5.8 3.2 + - - -
280B ARG* 4.3 21.7 - - - +
96F GLN* 3.7 40.0 + - + +
127F LEU* 3.5 3.1 - - - -
128F TYR* 2.8 39.7 + - + +
129F ALA* 2.6 31.1 + - + +
130F GLY* 1.3 75.2 - - - +
132F LYS* 1.3 66.1 + - - +
133F CYS* 3.8 3.0 + - + -
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Residues in contact with LYS 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLY* 6.0 2.5 - - - -
106A GLU* 3.4 32.4 + - - +
110A ARG* 5.0 14.9 - - - +
96F GLN* 4.0 2.8 - - - +
97F ASP* 3.0 47.3 + - + +
102F ARG* 4.6 1.8 - - - +
125F GLU* 3.0 35.0 + - + +
126F ASN 3.5 7.6 - - - +
127F LEU* 3.6 13.8 - - + +
130F GLY 4.0 0.2 + - - -
131F ARG* 1.3 74.4 - - - +
133F CYS* 1.3 65.4 + - - +
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Residues in contact with CYS 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ILE* 5.3 10.1 - - + -
94F MET* 5.9 1.1 - - - -
95F LEU 2.7 20.2 - - - +
96F GLN* 3.5 12.1 - - + -
97F ASP* 3.3 6.1 - - - +
124F TYR 3.6 0.3 - - - +
125F GLU* 3.4 2.5 - - - -
126F ASN* 3.0 39.0 + - - +
128F TYR* 4.0 28.7 - - - -
131F ARG* 4.4 4.0 - - + -
132F LYS* 1.3 78.0 - - - +
134F LEU* 1.3 63.7 + - - +
135F LEU* 3.8 20.3 + - - +
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Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F ILE* 4.8 1.3 - - + -
94F MET* 3.7 0.2 - - - -
95F LEU* 2.9 43.6 + - + +
97F ASP* 3.7 14.5 - - - +
101F ALA* 3.8 33.0 - - + +
102F ARG* 3.6 54.5 - - - +
105F VAL* 4.4 16.8 - - + -
123F VAL* 4.4 13.7 - - + -
124F TYR 3.2 9.4 - - - +
125F GLU* 4.1 10.5 - - + -
133F CYS* 1.3 71.7 - - - +
135F LEU* 1.3 63.3 + - - +
136F ILE* 4.1 2.3 + - + +
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Residues in contact with LEU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 4.5 5.8 - - + -
59F ILE* 3.6 33.7 - - + -
70F LEU* 4.8 9.2 - - + -
92F LEU* 4.1 12.3 - - + -
93F LYS 3.7 2.5 - - - -
94F MET* 3.5 29.8 - - + -
123F VAL* 3.5 3.8 - - - -
124F TYR* 2.7 48.5 + - + -
126F ASN* 4.1 20.6 - - + +
128F TYR* 6.2 0.9 - - + -
133F CYS* 3.9 25.4 - - - +
134F LEU* 1.3 85.4 - - - +
136F ILE* 1.3 62.2 + - - +
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Residues in contact with ILE 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ALA 3.6 1.2 - - - +
92F LEU* 3.4 4.1 - - - -
93F LYS* 2.7 58.3 + - + +
95F LEU* 4.1 19.5 - - + -
104F GLU* 4.4 11.9 - - + +
105F VAL* 3.5 35.2 - - + -
108F HIS* 5.5 2.7 - - - +
120F ILE* 4.0 37.0 - - + -
122F ASP 3.8 2.9 - - - +
123F VAL* 4.6 6.7 - - + +
134F LEU 5.0 1.8 - - - +
135F LEU* 1.3 76.4 - - - +
137F VAL* 1.3 64.2 + - - +
138F MET* 3.9 17.2 + - + +
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Residues in contact with VAL 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ILE* 3.9 17.9 - - + -
63F TYR* 3.8 29.6 - - + +
81F ILE* 4.5 4.5 - - + -
90F PHE* 3.8 26.2 - - + -
91F ALA 3.3 5.2 - - - +
92F LEU* 4.0 4.7 - - + -
120F ILE* 3.7 3.3 - - - +
121F VAL* 2.8 26.9 + - + +
122F ASP 2.9 18.3 + - - +
124F TYR* 3.7 31.2 - - + -
136F ILE* 1.3 73.9 - - - +
138F MET* 1.3 62.4 + - - +
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Residues in contact with MET 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F PDY 3.8 23.6 - - + -
78F VAL* 5.8 1.3 - - - -
90F PHE* 3.4 11.6 - - - +
91F ALA* 2.7 34.3 + - - +
93F LYS* 4.4 31.2 - - + -
104F GLU* 6.0 0.2 - - - +
108F HIS* 3.3 32.1 - - + +
118F VAL* 3.8 16.2 - - + -
119F ARG 3.2 15.5 - - - +
120F ILE* 4.4 2.2 - - + -
121F VAL* 4.3 1.1 - - - +
136F ILE* 4.2 17.9 - - + +
137F VAL* 1.3 78.1 - - - +
139F GLU* 1.3 74.7 + - - +
140F CYS 3.3 0.5 + - - -
207F ASP* 5.1 8.3 - - - +
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Residues in contact with GLU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F PDY 3.3 17.2 - - - -
90F PHE* 4.3 9.4 - - - -
118F VAL* 3.4 7.9 - - + -
119F ARG* 2.4 70.5 + - + +
121F VAL* 4.0 5.7 - - - +
138F MET* 1.3 72.6 - - - +
140F CYS* 1.3 61.8 + - - +
141F LEU* 4.1 13.0 - - + -
195F THR* 3.9 8.5 - - - +
204F LYS* 3.3 34.5 + - - +
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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