Contacts of the strand formed by residues 74 - 81 (chain A) in PDB entry 1TFZ
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 LEU 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 5.4 0.9 - - + -
49A MET* 3.9 21.2 - - + +
69A LEU 3.8 0.2 - - - +
70A THR* 3.2 8.5 - - - -
71A SER* 3.0 37.1 + - - +
73A ASP* 1.3 78.7 - - - +
75A ARG* 1.3 63.7 + - - +
76A PHE* 3.7 25.4 - - + -
200A ILE* 3.7 25.8 - - + -
201A ARG 3.4 2.4 + - - -
202A ARG* 4.0 11.9 - - - +
203A LEU* 3.8 35.0 - - + +
290A LEU* 3.8 23.1 - - + -
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Residues in contact with ARG 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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25A ARG* 6.0 2.0 - - - +
26A PHE 4.8 1.6 + - - -
27A HIS* 2.9 57.4 + - - +
28A HIS* 3.5 8.5 - - + +
29A ILE 3.2 21.1 + - - -
68A LEU* 4.0 13.2 - - + +
69A LEU 3.4 3.8 - - - -
70A THR* 4.0 13.9 - - + +
73A ASP* 3.6 16.0 + - - +
74A LEU* 1.3 80.8 - - - +
76A PHE* 1.3 68.2 + - - +
77A LEU 4.1 0.2 - - - -
171A TYR* 5.5 1.0 + - - -
180A GLU* 6.0 5.5 + - - +
181A PHE* 3.9 32.3 - - - +
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Residues in contact with PHE 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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29A ILE* 3.6 25.8 - - + -
31A PHE* 4.0 18.4 - + + -
43A PHE* 4.1 4.3 - + - -
47A LEU* 4.0 20.4 - - + -
49A MET* 3.6 27.5 - - + +
68A LEU* 3.6 3.2 - - - -
69A LEU* 2.8 37.1 + - + -
74A LEU* 3.7 22.4 - - + -
75A ARG* 1.3 82.7 - - - +
77A LEU* 1.3 59.7 + - - +
78A PHE* 3.5 27.6 - + + -
203A LEU* 5.3 0.2 - - + -
288A LEU* 3.8 20.0 - - + -
290A LEU* 3.8 22.0 - - + -
372A ILE* 4.3 8.7 - - + -
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Residues in contact with LEU 77 (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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28A HIS* 4.5 11.0 - - + +
29A ILE 2.8 16.6 + - - +
30A GLU* 3.4 21.3 - - + +
31A PHE* 2.8 35.3 + - - +
66A SER* 4.0 6.3 - - - -
67A TYR 3.6 17.5 - - - +
68A LEU* 4.1 10.1 - - + +
75A ARG 4.1 0.8 - - - -
76A PHE* 1.3 73.3 - - - +
78A PHE* 1.3 58.8 + - - +
79A THR* 3.9 7.6 - - - +
99A ILE* 3.7 29.6 - - + -
181A PHE* 4.0 20.6 - - + -
185A PHE* 3.7 28.5 - - + -
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Residues in contact with PHE 78 (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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31A PHE* 3.7 24.5 - + + -
33A CYS* 4.2 4.9 - - - -
36A ALA* 3.4 15.8 - - - +
39A VAL* 3.6 25.6 - - + -
40A ALA* 3.7 23.8 - - + -
43A PHE* 3.6 46.2 - + + -
66A SER* 3.2 2.8 - - - -
67A TYR 2.9 47.8 + - - +
69A LEU* 3.5 22.0 - - + -
76A PHE* 3.5 29.4 - + + -
77A LEU* 1.3 72.5 - - - +
79A THR* 1.3 62.4 + - - +
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Residues in contact with THR 79 (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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30A GLU* 2.7 30.3 + - - +
31A PHE 3.0 7.9 + - - -
32A TRP* 3.6 10.9 - - - +
33A CYS* 2.8 32.9 + - - +
36A ALA* 4.1 1.8 - - - -
64A HIS* 3.6 16.4 - - + +
65A ALA 3.2 3.6 - - - +
66A SER* 2.8 27.6 + - - +
77A LEU* 3.9 4.5 - - - +
78A PHE* 1.3 75.0 - - - +
80A ALA* 1.3 60.8 + - - +
99A ILE* 5.5 0.4 - - + -
102A PHE* 3.9 24.5 - - + -
107A CYS* 4.7 0.7 - - - -
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Residues in contact with ALA 80 (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 CYS 3.6 4.9 - - - +
34A GLY 3.5 19.1 - - - +
35A ASP* 4.2 0.4 - - - -
36A ALA* 3.5 28.7 - - + +
64A HIS* 3.4 6.2 - - - +
65A ALA* 2.8 37.0 + - + +
79A THR* 1.3 74.2 - - - +
81A PRO* 1.4 69.7 - - + +
102A PHE* 4.3 1.8 - - - -
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Residues in contact with PRO 81 (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 CYS 4.0 6.3 - - - +
34A GLY* 4.9 4.5 - - - +
63A VAL 3.8 2.5 - - - +
80A ALA* 1.4 89.0 - - + +
82A TYR* 1.3 63.9 + - - +
102A PHE* 3.4 16.2 - - + -
104A HIS* 3.2 27.4 - - + -
107A CYS* 3.5 23.3 - - - -
108A ARG* 3.3 37.2 + - + +
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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