Contacts of the strand formed by residues 54 - 66 (chain A) in PDB entry 1F95
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 TRP 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A MET* 3.2 37.0 - - + -
17A MET* 3.6 8.5 - - - -
43A LYS* 2.9 30.2 - - + +
46A PHE* 3.3 36.2 + + + -
47A ASP* 3.0 32.6 + - - +
50A TYR* 3.3 23.5 - + + +
51A ASN 3.0 28.1 + - - -
53A THR* 1.3 75.9 - - - +
55A HIS* 1.3 67.2 + - - +
72A HIS* 3.4 13.9 - + + -
85A LEU* 3.7 25.4 - - + -
86A PHE* 3.7 2.5 - - - -
87A LYS* 3.0 35.7 - - + +
65B TYR* 4.5 1.2 - - - +
66B VAL* 5.2 1.0 - - - -
67B THR 5.5 0.2 + - - -
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Residues in contact with HIS 55 (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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53A THR* 4.1 10.6 - - + +
54A TRP* 1.3 83.3 - - - +
56A CYS* 1.3 60.4 + - - +
57A ILE* 4.0 2.2 - - + -
85A LEU* 3.4 2.4 - - - +
86A PHE* 2.7 61.9 + - + +
88A SER* 3.1 32.7 + - - -
89A GLY 4.0 0.4 + - - -
55B HIS* 3.2 31.7 + + - -
65B TYR 3.9 3.8 - - - -
66B VAL* 4.3 18.9 - - + +
67B THR 3.8 11.0 + - - -
86B PHE* 4.5 2.8 - + - -
88B SER* 2.9 27.2 + - - -
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Residues in contact with CYS 56 (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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39A ALA* 3.1 35.9 - - + +
42A ILE* 3.7 31.4 - - - -
43A LYS* 4.2 8.0 - - + +
54A TRP 4.1 0.8 + - - -
55A HIS* 1.3 74.9 - - - +
57A ILE* 1.3 68.3 + - - +
58A VAL* 4.4 1.6 - - - -
83A ILE* 4.7 1.6 - - - -
84A LEU 3.1 18.2 - - - +
85A LEU* 3.8 12.3 - - + -
64B SER* 3.2 3.5 - - - -
65B TYR 2.9 35.7 + - - +
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Residues in contact with ILE 57 (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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55A HIS* 4.0 2.9 - - + -
56A CYS* 1.3 85.1 - - - +
58A VAL* 1.3 75.1 + - - +
62A PHE* 3.3 33.7 - - + -
64A SER* 5.4 0.2 - - - +
66A VAL* 6.3 0.2 - - + -
84A LEU* 2.7 47.9 + - + +
86A PHE* 3.6 33.4 - - + -
57B ILE* 4.1 17.7 - - + -
62B PHE* 4.1 12.1 - - + -
63B GLY 3.4 13.2 - - - +
64B SER* 3.4 14.8 - - - +
66B VAL* 5.0 3.6 - - + -
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Residues in contact with VAL 58 (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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29A LEU* 4.3 13.2 - - + -
35A GLU* 2.9 36.3 - - + +
38A ILE* 3.8 19.1 - - + -
39A ALA 4.2 5.8 - - - +
56A CYS* 4.4 3.8 - - - -
57A ILE* 1.3 88.1 - - - +
59A GLY* 1.3 54.3 + - - +
62A PHE* 4.9 0.2 - - - -
81A VAL* 4.4 9.2 - - + -
82A ALA 3.0 15.7 - - - +
83A ILE* 3.7 29.4 - - + -
62B PHE* 4.1 2.0 - - - -
63B GLY 2.6 42.0 + - - +
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Residues in contact with GLY 59 (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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35A GLU* 4.4 5.4 - - - -
58A VAL* 1.3 76.4 - - - +
60A ARG* 1.3 66.2 + - - -
61A ASN 3.2 2.8 + - - -
62A PHE* 3.7 7.9 - - - -
81A VAL* 4.7 4.0 - - - -
82A ALA* 2.9 35.5 + - - +
62B PHE* 3.4 22.0 - - - -
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Residues in contact with ARG 60 (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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35A GLU* 5.6 4.3 - - - +
59A GLY* 1.3 73.6 - - - -
61A ASN* 1.3 73.6 + - - +
80A GLN* 4.5 12.6 + - - +
81A VAL* 4.8 24.2 - - + +
61B ASN* 3.4 30.9 + - - +
9C THR* 4.1 7.2 + - - +
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Residues in contact with ASN 61 (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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59A GLY 3.2 1.4 - - - -
60A ARG* 1.3 89.9 - - - +
62A PHE* 1.3 68.5 + - - +
35B GLU* 5.1 2.5 - - - +
60B ARG* 3.3 50.8 + - - +
61B ASN* 3.2 18.8 + - - +
9C THR* 3.4 17.5 - - - +
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Residues in contact with PHE 62 (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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57A ILE* 3.3 37.9 - - + -
58A VAL 4.7 0.9 - - - -
59A GLY* 3.7 13.9 - - - -
61A ASN* 1.3 82.1 - - - +
63A GLY* 1.3 68.0 + - - +
64A SER* 4.4 4.0 - - - -
75A TYR* 4.3 12.8 - + - -
82A ALA* 3.5 32.1 - - + -
84A LEU* 5.1 1.1 - - + -
35B GLU* 3.5 10.9 + - - -
57B ILE* 3.8 17.9 - - + -
58B VAL 3.0 13.9 - - - +
59B GLY* 3.3 10.1 - - - -
62B PHE* 3.4 16.8 - + + -
7C THR* 4.2 15.0 - - - -
8C GLN* 3.3 9.4 + - - +
9C THR* 3.2 32.7 + - + -
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Residues in contact with GLY 63 (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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62A PHE* 1.3 78.6 - - - +
64A SER* 1.3 58.2 + - - -
35B GLU* 3.0 18.6 - - - +
36B LYS* 3.7 6.5 - - - -
39B ALA* 3.5 3.1 - - - +
57B ILE* 3.5 1.4 - - - +
58B VAL* 2.6 43.0 + - - +
7C THR 3.0 14.4 - - - -
8C GLN* 4.1 0.7 - - - -
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Residues in contact with SER 64 (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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57A ILE* 5.4 0.2 - - - +
62A PHE* 4.4 3.1 - - - -
63A GLY* 1.3 75.5 - - - -
65A TYR* 1.3 59.1 + - - +
66A VAL* 4.5 6.8 - - - +
84A LEU* 4.2 7.6 - - - +
35B GLU 4.4 0.4 + - - -
36B LYS* 4.4 0.8 - - - +
39B ALA* 3.5 4.9 - - - -
56B CYS 3.0 18.4 - - - -
57B ILE* 3.4 25.5 - - - +
5C LYS 3.9 1.0 - - - +
6C SER* 3.0 6.7 + - - -
7C THR* 2.5 64.3 + - - +
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Residues in contact with TYR 65 (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 SER* 1.3 71.8 - - - +
66A VAL* 1.3 81.7 + - - +
39B ALA* 3.7 3.7 - - - +
40B ALA* 3.3 46.0 - - + +
43B LYS* 3.2 36.4 + - + +
44B LYS* 3.8 27.6 - - + -
55B HIS* 4.0 0.2 - - - -
56B CYS 2.9 22.0 + - - -
4C ASP* 2.7 51.7 + - + -
5C LYS 4.0 11.7 - - - -
6C SER* 4.1 8.1 - - - +
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Residues in contact with VAL 66 (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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55A HIS* 5.7 0.4 - - - +
64A SER* 4.5 9.2 - - - +
65A TYR* 1.3 89.5 - - - +
67A THR* 1.3 63.3 + - - +
68A HIS* 4.2 1.7 + - - -
73A PHE* 5.5 3.6 - - + -
84A LEU* 4.6 8.5 - - + -
86A PHE* 3.0 45.5 - - + -
43B LYS* 4.3 5.4 - - - +
55B HIS* 4.0 23.3 - - + +
56B CYS 4.3 7.6 - - - +
57B ILE* 5.0 6.5 - - + -
4C ASP* 4.3 1.6 - - - -
5C LYS* 2.8 44.0 + - - +
7C THR* 5.0 1.1 - - + -
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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