Contacts of the strand formed by residues 138 - 147 (chain A) in PDB entry 2F2D
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 CYS 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A THR* 4.0 1.9 - - - +
73A SER* 2.8 55.6 + - - +
74A LEU 3.8 14.8 - - - -
75A GLU* 4.5 3.1 - - - +
113A MET* 3.7 34.1 - - + -
114A VAL 3.5 6.1 - - - +
115A THR* 4.0 14.4 - - + +
136A ALA 4.2 0.6 + - - -
137A LEU* 1.3 71.4 - - - +
139A LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.8 28.0 - - + -
71A GLN 3.5 7.9 - - - +
72A THR* 4.3 6.5 - - - +
96A ILE* 4.4 3.1 - - + -
98A ALA* 5.3 0.2 - - + -
99A LEU* 3.6 30.7 - - + -
113A MET* 5.0 1.3 - - - +
114A VAL* 3.1 44.3 + - + +
116A ALA* 4.1 7.6 - - + -
121A CYS* 3.5 32.1 - - - -
122A TYR* 4.2 8.5 - - + +
137A LEU* 3.9 17.7 - - + +
138A CYS* 1.3 75.2 - - - +
140A GLU* 1.3 63.6 + - - +
141A VAL* 3.6 3.8 + - + -
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A HIS 3.0 16.5 - - - +
70A LEU* 3.6 1.8 - - - -
71A GLN* 3.2 49.2 + - + +
111A THR* 3.6 29.3 - - + +
112A ALA 3.6 17.3 - - - +
113A MET* 4.3 19.6 + - + +
139A LEU* 1.3 69.9 - - - +
141A VAL* 1.3 61.8 + - - +
142A THR* 3.8 7.8 + - - +
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 4.4 5.6 - - - +
68A VAL* 3.9 20.6 - - + -
69A HIS 3.8 3.6 - - - -
70A LEU* 4.5 5.2 - - + +
99A LEU* 3.8 42.0 - - + -
106A MET* 5.2 2.0 - - - -
110A GLU* 3.7 27.8 - - - +
112A ALA 3.0 31.5 + - - +
114A VAL* 3.6 25.4 - - + -
139A LEU* 3.8 9.9 - - + +
140A GLU* 1.3 70.9 - - - +
142A THR* 1.3 60.5 + - - +
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Residues in contact with THR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 4.6 1.1 - - - -
69A HIS* 3.0 56.4 + - + +
110A GLU 3.3 15.9 - - - +
111A THR* 3.6 28.1 - - + +
140A GLU* 4.1 10.4 + - - +
141A VAL* 1.3 72.2 - - - +
143A LEU* 1.3 66.0 + - - +
144A LYS* 3.3 6.4 + - + +
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO* 5.9 0.4 - - + -
66A VAL* 5.0 2.7 - - + -
67A THR 3.7 16.8 - - - +
68A VAL* 3.8 8.7 - - + +
106A MET* 3.7 44.0 - - + +
107A ASP 4.4 0.9 - - - +
108A VAL* 3.8 40.6 - - + -
109A GLY* 3.6 22.2 - - - +
110A GLU* 3.4 30.4 + - + +
141A VAL 4.0 0.2 - - - -
142A THR* 1.3 70.8 - - - +
144A LYS* 1.3 64.2 + - - +
145A THR 3.8 17.9 - - - +
146A ALA* 4.1 3.8 - - + +
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A THR* 3.2 16.6 + - + +
68A VAL 4.3 2.5 - - - -
69A HIS* 4.0 20.6 - - + +
84A PRO 3.4 24.9 - - - -
85A GLU* 2.6 36.9 + - - -
108A VAL* 5.1 4.0 - - - +
109A GLY* 5.5 0.7 + - - -
142A THR* 3.3 16.1 + - + +
143A LEU* 1.3 76.2 - - - +
145A THR* 1.4 72.6 + - + +
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Residues in contact with THR 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 4.0 0.3 - - - -
67A THR* 3.0 45.4 + - - +
108A VAL* 5.1 2.2 - - - -
143A LEU* 3.8 5.5 - - - +
144A LYS* 1.4 86.8 - - + +
146A ALA* 1.3 59.8 + - - +
147A VAL* 3.9 21.9 + - + +
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PRO* 4.3 13.2 - - + -
64A GLN* 4.0 10.3 + - - +
66A VAL* 4.1 21.8 - - + -
108A VAL* 3.7 34.4 - - + +
143A LEU* 4.1 6.6 - - + +
145A THR* 1.3 71.2 - - - +
147A VAL* 1.3 62.7 + - - +
148A ASP* 4.4 0.5 + - - +
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLN* 4.4 2.9 - - - +
65A VAL* 2.9 44.5 + - + +
67A THR* 4.8 4.5 - - - +
87A VAL* 6.1 0.4 - - + -
145A THR* 4.3 25.4 - - + +
146A ALA* 1.3 75.8 - - - +
148A ASP* 1.3 61.5 + - - +
149A GLY 3.2 4.0 + - - -
150A PRO* 4.0 30.7 - - + -
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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