Contacts of the strand formed by residues 63 - 76 (chain A) in PDB entry 1FNA
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 LYS 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PRO 3.5 3.4 - - - +
38A GLU* 2.7 35.3 + - - +
61A GLY 5.7 0.9 - - - +
62A LEU* 1.3 74.3 - - - +
64A PRO* 1.3 65.9 - - + +
66A VAL* 3.6 24.5 - - + +
68A TYR* 2.9 15.2 + - - +
94A THR* 2.5 25.5 + - - -
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Residues in contact with PRO 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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15A PRO* 3.3 27.1 - - + +
16A THR* 4.1 10.1 - - + -
62A LEU 4.2 3.1 - - - +
63A LYS* 1.3 91.8 - - + +
65A GLY* 1.3 61.2 + - - +
66A VAL* 3.5 7.6 + - - +
94A THR* 3.6 0.2 - - - +
95A GLU 3.5 11.7 - - - +
96A ILE* 4.3 15.4 - - + +
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Residues in contact with GLY 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 PRO* 1.3 71.7 - - - +
66A VAL* 1.3 61.4 - - - +
93A ARG* 3.9 19.1 + - - +
94A THR* 3.0 22.9 + - - -
95A GLU 3.3 4.9 + - - -
96A ILE* 3.8 19.2 - - - +
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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
----------------------------------------------------------
38A GLU* 4.0 22.4 - - + +
63A LYS* 3.6 31.0 - - + +
64A PRO 3.5 14.8 - - - +
65A GLY* 1.3 79.8 - - - +
67A ASP* 1.4 74.6 + - - +
68A TYR* 3.4 26.9 - - + +
93A ARG* 3.3 3.4 - - - -
94A THR* 3.0 25.0 + - - -
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Residues in contact with ASP 67 (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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38A GLU* 3.6 5.5 - - - -
39A THR* 2.6 63.4 + - + +
66A VAL* 1.4 76.5 - - - +
68A TYR* 1.3 57.3 + - - +
91A ASN* 3.0 25.2 + - - +
92A TYR 3.6 14.3 + - - -
93A ARG* 4.0 13.7 + - + +
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Residues in contact with TYR 68 (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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18A LEU* 5.8 1.8 - - + -
36A TYR* 4.5 10.1 - + + -
37A GLY* 3.3 22.0 - - - +
38A GLU* 3.7 22.0 + - + +
39A THR* 3.3 5.6 - - - -
61A GLY 5.0 0.3 + - - -
62A LEU* 3.5 38.1 - - + -
63A LYS* 2.9 42.0 + - - +
66A VAL* 3.4 31.6 - - + +
67A ASP* 1.3 74.2 - - - +
69A THR* 1.3 59.0 + - - +
70A ILE* 4.0 20.2 + - + +
90A ILE 3.7 0.3 - - - +
91A ASN* 3.2 5.4 - - - -
92A TYR 2.8 37.1 + - - +
94A THR* 4.1 9.4 - - + -
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Residues in contact with THR 69 (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 THR 3.9 0.5 - - - +
36A TYR* 3.2 4.9 - - - +
37A GLY 2.9 31.4 + - - -
39A THR* 2.7 28.1 + - - +
68A TYR* 1.3 71.2 - - - +
70A ILE* 1.3 62.3 + - - +
71A THR* 4.3 13.2 + - - +
89A SER* 5.1 6.5 - - - -
90A ILE 3.5 6.7 - - - +
91A ASN* 2.8 16.4 + - - +
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Residues in contact with ILE 70 (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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8A LEU* 3.7 9.2 - - + +
10A VAL* 4.9 0.2 - - + -
18A LEU* 4.3 23.3 - - + -
20A ILE* 4.0 32.8 - - + -
34A ILE* 4.3 4.9 - - + -
35A THR 3.5 8.5 - - - +
36A TYR* 4.0 12.6 - - + -
59A ILE* 4.1 20.6 - - + -
68A TYR* 4.3 14.8 - - + +
69A THR* 1.3 78.7 - - - +
71A THR* 1.4 68.5 + - - +
89A SER* 3.2 2.4 - - - -
90A ILE* 2.8 45.8 + - + +
92A TYR* 4.6 16.6 - - + -
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Residues in contact with THR 71 (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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33A ARG 3.7 0.9 - - - +
34A ILE* 3.4 5.2 - - - +
35A THR* 2.8 47.2 + - - +
69A THR* 4.3 10.0 + - - +
70A ILE* 1.4 77.1 - - - +
72A VAL* 1.3 67.6 + - - +
73A TYR* 3.5 27.9 + - + +
87A PRO* 3.7 18.4 - - + -
88A ILE 3.3 7.4 - - - +
89A SER* 2.6 26.2 + - - +
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Residues in contact with VAL 72 (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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8A LEU* 4.2 27.1 - - + -
20A ILE* 4.5 5.4 - - + -
22A TRP* 4.1 29.4 - - + +
32A TYR* 3.7 33.2 - - + -
33A ARG 3.4 4.3 - - - +
34A ILE* 4.3 12.6 - - + -
71A THR* 1.3 80.3 - - - +
73A TYR* 1.3 66.7 + - - +
74A ALA 4.5 0.2 + - - -
86A LYS 4.5 1.2 - - - +
87A PRO* 3.4 4.7 - - - +
88A ILE* 2.8 43.4 + - + +
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Residues in contact with TYR 73 (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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32A TYR* 3.2 6.8 - - - +
33A ARG* 2.9 72.9 + - + +
35A THR* 4.0 21.8 + - + -
71A THR* 3.5 24.1 - - + +
72A VAL* 1.3 79.9 - - - +
74A ALA* 1.3 63.8 + - - +
75A VAL* 5.2 1.1 - - + -
85A SER 4.9 3.6 - - - +
87A PRO* 3.6 33.7 - - + +
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Residues in contact with ALA 74 (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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25A PRO* 4.0 5.4 - - + -
29A VAL* 4.0 16.4 - - + -
31A TYR 3.9 3.4 - - - -
32A TYR* 3.9 23.3 - - + -
73A TYR* 1.3 75.4 - - - +
75A VAL* 1.3 63.5 + - - +
76A THR* 5.2 1.6 - - + -
84A SER* 2.9 24.7 - - - -
85A SER* 3.7 31.5 + - - +
86A LYS 5.7 0.2 + - - -
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Residues in contact with VAL 75 (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 VAL* 3.7 1.9 - - - +
30A ARG* 2.8 24.7 + - + +
31A TYR* 2.8 65.9 + - + +
33A ARG* 4.0 20.2 - - + +
73A TYR* 4.9 3.1 - - + +
74A ALA* 1.3 78.1 - - - +
76A THR* 1.3 71.1 + - - +
80A ASP* 3.9 28.9 - - + +
84A SER* 4.1 4.0 - - - +
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Residues in contact with THR 76 (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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27A VAL* 3.5 31.2 - - + -
28A THR 3.6 11.4 - - - +
29A VAL* 4.9 2.0 - - + -
30A ARG* 4.0 9.1 - - - +
74A ALA 5.0 1.8 - - - +
75A VAL* 1.3 88.2 - - - +
77A GLY* 1.3 62.1 - - - +
78A ARG* 3.0 31.3 + - - +
79A GLY 4.1 17.7 + - - +
80A ASP* 5.6 0.5 - - - +
83A ALA 4.8 1.7 + - - -
84A SER* 4.0 26.0 + - - +
85A SER* 5.0 0.9 - - - +
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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