Contacts of the strand formed by residues 25 - 36 (chain F) in PDB entry 3OF6
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 GLN 25 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18F MET* 3.2 41.3 - - + +
19F LEU 3.5 9.9 - - - +
20F LEU* 4.4 4.3 - - + +
23F GLY 4.5 0.2 + - - -
24F LYS* 1.3 74.7 - - - +
26F GLN* 1.3 65.0 + - - +
79F PRO* 4.2 1.0 - - - +
80F SER* 3.2 46.7 + - - +
81F GLU* 5.6 2.5 - - - +
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Residues in contact with GLN 26 (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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18F MET* 3.6 6.8 - - - -
19F LEU* 2.8 43.5 + - + +
21F VAL* 3.6 30.9 - - + +
24F LYS* 3.5 4.4 + - - +
25F GLN* 1.3 76.7 - - - +
27F MET* 1.3 61.8 + - - +
28F VAL* 3.6 9.6 + - + +
77F SER* 2.8 29.8 + - - +
78F LEU* 3.1 7.7 - - - +
79F PRO* 3.1 43.3 - - - +
80F SER* 4.0 2.5 - - - -
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Residues in contact with MET 27 (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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16F PRO* 3.4 38.6 - - + -
17F ILE 3.9 5.4 - - - +
18F MET* 4.1 15.5 - - + -
26F GLN* 1.3 69.2 - - - +
28F VAL* 1.3 63.7 + - - +
29F VAL* 3.6 27.1 - - + +
76F LEU 3.6 2.0 - - - +
77F SER* 3.7 0.3 - - - -
78F LEU* 2.7 59.6 + - + +
79F PRO 4.7 0.7 - - - +
80F SER* 3.7 12.7 + - - +
83F LEU* 4.5 12.1 - - + -
89F LEU* 4.5 6.5 - - + -
107F MET* 5.1 0.2 - - + -
109F LEU* 3.8 31.2 - - + -
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Residues in contact with VAL 28 (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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131C PHE* 3.5 22.1 - - + -
149C LEU* 5.4 1.8 - - + -
16F PRO* 3.5 2.1 - - - +
17F ILE* 2.8 47.1 + - + -
19F LEU* 3.7 26.2 - - + -
26F GLN* 4.1 19.7 - - + +
27F MET* 1.3 81.5 - - - +
29F VAL* 1.3 67.9 + - - +
75F HIS* 4.7 13.7 - - + -
76F LEU 3.2 11.2 - - - +
77F SER* 4.2 9.2 - - - +
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Residues in contact with VAL 29 (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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131C PHE* 4.4 6.1 - - - -
13F LEU* 4.4 7.4 - - + -
14F ALA 3.6 18.8 - - - +
16F PRO* 4.5 3.1 - - + -
27F MET* 3.6 14.3 - - + +
28F VAL* 1.3 74.8 - - - +
30F VAL* 1.3 73.7 + - - +
47F PHE* 4.1 9.4 - - + -
75F HIS* 3.2 7.1 - - - +
76F LEU* 2.8 50.0 + - + +
89F LEU* 3.5 22.9 - - + -
107F MET* 3.8 23.3 - - + -
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Residues in contact with VAL 30 (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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131C PHE* 3.6 37.5 - - + -
147C VAL* 4.4 13.0 - - + -
149C LEU* 4.8 2.2 - - + -
13F LEU* 3.7 7.6 - - - +
14F ALA* 3.1 38.6 + - + +
29F VAL* 1.3 80.6 - - - +
31F CYS* 1.3 63.5 + - - +
32F LEU* 4.3 1.5 + - + -
47F PHE* 4.5 0.7 - - - -
73F LEU* 3.5 30.7 - - + -
74F ALA 3.2 15.3 - - - +
75F HIS* 4.1 7.6 - - + +
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Residues in contact with CYS 31 (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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11F PRO* 4.7 4.3 - - - -
12F SER 3.5 20.9 - - - -
13F LEU* 3.6 3.8 - - + -
30F VAL* 1.3 73.6 - - - +
32F LEU* 1.3 65.0 + - - +
33F VAL* 4.1 1.1 - - - -
45F ILE* 3.8 12.5 - - + +
47F PHE* 3.5 17.9 - - + -
73F LEU* 3.4 6.4 - - - +
74F ALA 2.8 32.2 + - - -
91F CYS* 2.0 47.3 - - - -
93F THR* 5.9 0.4 - - - -
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Residues in contact with LEU 32 (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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137C GLU* 5.5 1.8 - - - +
145C THR* 3.6 33.2 - - + +
147C VAL* 4.1 15.0 - - + -
196C ARG* 3.9 20.6 - - - -
10F PHE 3.4 3.3 - - - +
12F SER* 2.8 47.4 + - - +
14F ALA* 6.5 0.9 - - + -
30F VAL* 5.5 1.1 - - + -
31F CYS* 1.3 74.3 - - - +
33F VAL* 1.3 59.3 + - - +
34F LEU* 3.7 20.9 + - + +
71F THR* 3.9 13.9 - - - -
72F ASN 3.3 18.4 - - - +
73F LEU* 3.6 18.4 - - + -
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Residues in contact with VAL 33 (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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9F PRO* 3.5 31.4 - - + -
10F PHE 3.2 11.9 - - - +
11F PRO* 4.2 2.5 - - + -
31F CYS* 4.1 2.3 - - - -
32F LEU* 1.3 71.2 - - - +
34F LEU* 1.3 64.1 + - - +
36F VAL* 3.3 12.1 - - + +
43F SER* 4.3 3.4 - - - +
45F ILE* 3.7 9.6 - - + +
71F THR* 3.4 5.0 - - - -
72F ASN* 3.1 48.9 + - + +
93F THR* 3.6 33.2 - - + +
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Residues in contact with LEU 34 (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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137C GLU* 3.6 29.2 - - + +
141C THR* 4.5 4.7 - - + -
145C THR* 4.7 4.0 - - + +
198C ARG* 3.3 33.4 - - - +
9F PRO* 3.2 2.9 - - - +
10F PHE* 2.9 51.3 + - + +
12F SER* 4.9 2.7 - - - +
32F LEU* 3.7 33.2 - - + +
33F VAL* 1.3 74.1 - - - +
35F ASP* 1.3 71.8 + - + +
36F VAL* 3.4 3.1 + - - +
71F THR* 3.6 23.1 - - + -
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Residues in contact with ASP 35 (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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8F THR* 3.1 36.0 + - - +
9F PRO* 3.6 15.2 - - - +
10F PHE* 4.9 1.8 - - + +
34F LEU* 1.3 80.6 - - + +
36F VAL* 1.3 61.5 + - - +
69F THR* 4.3 23.1 + - - +
70F TRP 3.5 5.9 + - - -
71F THR* 4.4 1.8 - - - +
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Residues in contact with VAL 36 (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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9F PRO* 5.0 4.7 - - + -
33F VAL* 3.3 36.3 - - + +
34F LEU 3.7 6.7 - - - +
35F ASP* 1.3 75.2 - - - +
37F ALA* 1.3 80.5 + - - +
39F PRO* 5.4 0.2 - - + -
41F LEU 5.9 0.9 - - - +
42F ASP* 5.3 1.1 - - - +
43F SER* 3.7 28.0 - - - +
62F PRO* 5.1 9.4 - - + -
69F THR* 4.2 2.4 - - - -
70F TRP* 2.7 48.8 + - + +
71F THR* 3.7 6.5 - - - +
72F ASN* 3.9 6.3 - - + +
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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