Contacts of the strand formed by residues 89 - 99 (chain A) in PDB entry 4FPR
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 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLU* 3.4 20.9 - - - +
31A ILE 3.8 1.8 - - - -
32A ARG* 3.1 29.8 - - + +
76A CYS* 3.6 0.9 - - - -
77A ALA* 3.2 32.8 + - + +
87A VAL* 3.5 16.6 + - + +
88A VAL* 1.3 75.8 - - - +
90A CYS* 1.3 62.4 + - - +
123A THR* 3.5 31.6 - - + +
135D MET* 4.1 27.1 - - + +
136D LYS* 3.9 8.8 - - + +
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Residues in contact with CYS 90 (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 GLY 3.8 0.2 - - - +
30A GLU* 3.2 9.3 - - - +
31A ILE* 2.8 48.0 + - + +
33A TYR* 3.6 28.7 - - + +
39A PRO* 4.9 0.4 - - - -
44A ALA* 4.0 5.4 - - + -
74A VAL* 3.9 10.8 - - + -
75A GLN 3.3 4.3 - - - +
76A CYS* 2.0 45.8 - - - -
88A VAL* 4.2 4.7 - - - -
89A LEU* 1.3 77.0 - - - +
91A THR* 1.3 60.3 + - - +
92A CYS* 3.8 1.2 + - + +
136D LYS* 5.1 0.2 - - - -
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Residues in contact with THR 91 (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 SER* 4.6 7.0 - - - +
29A GLY 3.5 9.2 - - - +
30A GLU* 4.7 4.1 + - - +
74A VAL* 3.2 7.0 - - - +
75A GLN* 2.8 35.7 + - + -
89A LEU 4.2 0.8 + - - -
90A CYS* 1.3 71.9 - - - +
92A CYS* 1.3 70.1 + - - +
93A LYS* 4.2 4.5 + - + +
122A GLU* 3.9 24.0 + - - +
136D LYS* 2.8 41.3 + - - +
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Residues in contact with CYS 92 (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 ILE 4.0 0.3 - - - +
28A SER* 3.3 5.5 - - - -
29A GLY 2.8 36.3 + - - +
31A ILE* 4.4 13.5 - - + -
48A CYS* 2.0 57.4 - - + -
51A VAL* 4.3 4.3 - - - -
73A LYS 3.8 1.1 - - - -
74A VAL* 4.4 2.9 - - + -
90A CYS* 3.8 1.7 + - + +
91A THR* 1.3 74.5 - - - +
93A LYS* 1.3 58.7 + - - +
94A ILE* 3.3 19.1 - - - -
119A PHE* 4.2 13.5 - - + -
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Residues in contact with LYS 93 (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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26A SER* 3.6 30.3 - - - +
27A ILE 3.5 4.3 - - - +
28A SER* 3.5 19.3 - - - +
71A THR 3.8 1.0 - - - +
72A ALA* 3.6 2.9 - - - -
73A LYS* 3.1 46.0 + - + +
91A THR* 4.2 5.6 + - + +
92A CYS* 1.3 76.8 - - - +
94A ILE* 1.3 64.8 + - - +
95A THR* 4.0 7.0 + - - +
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Residues in contact with ILE 94 (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 ALA 4.0 0.2 - - - +
26A SER* 3.1 4.9 + - - -
27A ILE* 2.9 42.6 + - + +
48A CYS* 4.0 3.4 - - - -
51A VAL* 3.5 23.3 - - + -
52A THR* 3.5 24.5 - - + +
55A LEU* 4.2 7.9 - - + -
70A MET* 4.0 37.2 - - + -
71A THR 3.5 5.2 - - - +
72A ALA* 4.4 2.5 - - + -
92A CYS* 3.3 33.2 - - - -
93A LYS* 1.3 74.4 - - - +
95A THR* 1.3 65.6 + - - +
96A ALA 4.1 0.2 + - - -
119A PHE* 4.2 8.1 - - + -
131A TRP* 4.2 3.7 - - + -
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Residues in contact with THR 95 (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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24A GLU* 3.7 26.4 + - + +
25A ALA 3.3 9.4 - - - +
26A SER* 2.6 17.0 + - - +
70A MET* 3.3 3.6 - - - -
71A THR* 2.9 35.9 + - - -
73A LYS* 6.0 3.5 - - - +
93A LYS* 4.0 10.8 + - - +
94A ILE* 1.3 76.4 - - - +
96A ALA* 1.3 60.8 + - - +
97A HIS* 3.5 30.5 - - + +
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Residues in contact with ALA 96 (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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23A ARG 3.9 1.4 - - - +
24A GLU* 3.5 2.4 - - - +
25A ALA 2.5 37.9 + - - +
66A TRP 3.6 22.7 - - - +
69A ASP 3.7 4.7 - - - -
70A MET* 4.1 7.4 - - + -
94A ILE 4.1 1.2 - - - -
95A THR* 1.3 71.9 - - - +
97A HIS* 1.3 62.9 + - - +
98A ARG 3.6 0.2 - - - -
99A TYR* 4.2 12.6 - - + +
131A TRP* 3.7 28.8 - - + -
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Residues in contact with HIS 97 (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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23A ARG 3.5 2.9 - - - +
24A GLU* 4.4 11.2 + - - +
69A ASP* 2.9 43.4 + - + +
70A MET* 4.2 0.7 - - - -
71A THR* 2.7 28.7 + - - -
95A THR* 3.5 28.5 + - + +
96A ALA* 1.3 73.2 - - - +
98A ARG* 1.3 65.8 + - + +
99A TYR 3.7 0.9 - - - -
140A ARG* 2.8 39.4 + - - +
41B LYS* 3.4 44.3 - - + +
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Residues in contact with ARG 98 (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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22A CYS* 3.5 14.9 - - + -
66A TRP 4.2 5.2 + - - -
67A GLY* 3.6 22.5 + - - -
68A ILE 5.8 1.1 - - - +
69A ASP* 4.4 19.1 + - + +
97A HIS* 1.3 87.0 - - + +
99A TYR* 1.3 62.7 + - - +
100A ARG* 3.9 3.3 + - - +
140A ARG* 4.3 10.5 - - + +
141A GLY* 2.9 45.0 + - - +
142A CYS 3.9 13.7 - - - +
143A ASP 3.3 23.1 + - - -
144A HIS* 3.1 44.4 + - - +
145A HIS 5.1 1.2 - - - +
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Residues in contact with TYR 99 (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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22A CYS* 2.9 19.6 - - - +
23A ARG* 3.0 26.8 + - + +
25A ALA* 3.5 26.5 - - + -
65A ALA 4.1 0.7 - - - -
66A TRP* 3.4 48.5 + + + -
96A ALA* 4.2 9.2 - - + +
98A ARG* 1.3 74.8 - - - +
100A ARG* 1.3 63.5 + - - +
101A GLU* 3.4 29.0 + - + -
103A VAL 5.5 1.1 + - - -
105A LYS* 4.5 23.0 - - - +
106A ILE 5.0 0.2 + - - -
131A TRP* 3.7 34.9 - + + +
133A VAL* 3.7 19.1 - - + +
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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