Contacts of the strand formed by residues 81 - 94 (chain F) in PDB entry 3B4V
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 CYS 81 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77E LEU* 5.5 3.2 - - + +
116E SER* 5.6 0.2 - - - -
11F CYS* 2.0 56.3 - - + -
12F CYS 3.8 2.0 - - - -
40F CYS* 3.7 19.5 - - - +
41F GLU* 3.6 24.2 - - - -
42F GLY 3.6 23.0 + - - +
44F CYS* 3.5 5.2 - - - +
80F CYS* 1.3 70.3 - - - +
82F VAL* 1.3 65.3 + - - +
113F CYS* 4.4 0.2 - - - -
114F GLY 3.8 0.2 - - - -
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Residues in contact with VAL 82 (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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80E CYS* 4.2 1.1 - - + -
82E VAL* 3.7 43.3 - - + -
83E PRO* 5.3 2.0 - - + +
116E SER* 3.6 23.8 - - - +
40F CYS* 3.4 6.7 - - - -
80F CYS* 3.8 18.6 - - + +
81F CYS* 1.3 79.5 - - - +
83F PRO* 1.3 83.4 - - + +
84F THR* 5.3 3.1 - - + -
113F CYS* 3.5 1.9 - - - -
114F GLY 3.0 35.3 + - - +
115F CYS 5.1 0.2 - - - -
116F SER* 4.1 7.2 - - - +
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Residues in contact with PRO 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E HIS* 4.6 9.2 - - + +
60E SER* 6.1 0.2 - - - +
82E VAL* 5.4 1.7 - - + +
83E PRO 4.2 11.1 - - - +
84E THR* 5.5 1.9 - - - -
116E SER* 4.1 18.8 - - - +
40F CYS* 3.3 10.7 - - + +
82F VAL* 1.3 95.3 - - + +
84F THR* 1.3 62.9 + - - +
85F LYS 4.6 0.7 - - - +
86F LEU* 3.9 28.9 - - + -
110F VAL* 3.9 24.5 - - + -
112F GLU 3.5 7.9 - - - +
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Residues in contact with THR 84 (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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83E PRO 5.6 2.5 - - - +
84E THR* 5.1 8.1 - - - +
86E LEU* 5.7 12.1 - - + +
1F GLY 5.5 0.3 + - - -
57F SER* 6.2 4.3 - - - +
82F VAL* 3.4 4.4 + - + +
83F PRO* 1.3 75.7 - - - +
85F LYS* 1.3 62.3 + - - +
112F GLU* 2.8 33.8 + - - +
113F CYS 3.8 3.8 + - - -
114F GLY* 3.7 27.6 - - - +
115F CYS 5.5 3.1 - - - +
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Residues in contact with LYS 85 (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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83F PRO 3.6 0.6 - - - -
84F THR* 1.3 81.1 - - - +
86F LEU* 1.3 70.8 + - - +
87F ARG* 5.8 0.4 - - + -
110F VAL* 3.6 4.2 - - - +
111F GLU* 2.6 46.7 + - + -
112F GLU* 3.4 44.7 + - + +
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Residues in contact with LEU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E SER* 4.3 11.4 - - - +
59E HIS* 4.1 13.9 - - + -
84E THR* 5.9 9.2 - - + -
83F PRO* 3.9 22.2 - - + -
85F LYS* 1.3 83.1 - - - +
87F ARG* 1.3 64.1 + - - +
107F ASN* 3.8 45.3 - - + +
109F ILE 3.1 18.6 - - - +
110F VAL* 3.8 20.6 - - + +
111F GLU 5.0 0.4 - - - -
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Residues in contact with ARG 87 (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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85F LYS* 5.8 0.9 - - + -
86F LEU* 1.3 75.7 - - - +
88F PRO* 1.3 80.2 + - + +
106F GLN* 5.2 0.7 - - - -
107F ASN 4.3 3.8 - - - +
108F MET 3.1 19.8 + - - -
109F ILE* 2.9 55.5 + - + +
111F GLU* 2.8 41.6 + - + +
129G GLY* 2.9 30.3 + - - -
130G HIS* 3.7 28.1 + - - +
131G PRO* 4.9 3.2 - - - +
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Residues in contact with PRO 88 (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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87F ARG* 1.3 105.5 + - + +
89F MET* 1.3 62.9 + - - +
104F ASP* 4.3 17.7 - - + +
105F ILE 3.2 17.9 - - - +
106F GLN* 3.5 40.8 - - - +
108F MET* 4.5 0.4 - - - -
109F ILE* 4.1 4.0 - - - +
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Residues in contact with MET 89 (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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32F PRO* 4.3 20.2 - - + -
35F TYR* 3.7 33.7 - - + -
88F PRO* 1.3 74.1 - - - +
90F SER* 1.3 73.5 + - - +
91F MET* 3.6 6.0 + - - +
104F ASP* 4.1 4.0 - - - -
105F ILE 2.8 30.1 + - - +
108F MET* 3.8 18.8 - - + -
109F ILE* 4.2 16.4 - - + -
132G ASP* 4.0 29.4 - - + +
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Residues in contact with SER 90 (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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32F PRO* 4.3 8.0 - - - +
89F MET* 1.3 83.6 - - - +
91F MET* 1.3 65.7 + - - +
102F LYS* 3.3 34.6 - - - +
103F LYS 3.6 2.6 + - - -
104F ASP* 3.1 23.7 + - - -
111G SER 6.2 0.4 - - - -
112G ASP* 5.3 10.8 - - - -
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Residues in contact with MET 91 (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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58E PHE* 4.1 11.2 - - + -
20F PHE* 4.0 8.5 - - + -
29F ILE* 3.6 37.2 - - + -
31F ALA 4.0 2.5 - - - +
32F PRO* 3.8 23.6 - - - -
89F MET* 3.7 12.1 - - - +
90F SER* 1.3 80.4 + - - +
92F LEU* 1.3 61.2 + - - +
93F TYR* 3.6 8.0 - - + -
101F ILE 3.3 2.4 - - - +
102F LYS* 3.2 6.6 - - - -
103F LYS 2.8 36.9 + - - +
105F ILE* 4.1 14.4 - - + -
108F MET* 3.7 33.9 - - + -
61H LEU* 4.9 5.4 - - + -
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Residues in contact with LEU 92 (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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29F ILE* 3.5 2.9 - - - +
30F ILE* 2.6 39.6 + - + -
31F ALA* 2.9 24.3 + - + +
91F MET* 1.3 71.9 - - - +
93F TYR* 1.3 58.2 + - - +
100F ILE* 3.4 28.7 - - + -
101F ILE 3.3 14.4 - - - +
102F LYS* 3.9 14.1 - - + +
157G VAL* 4.0 12.8 - - + -
159G ASP* 4.0 6.3 - - + -
165G HIS* 3.9 28.7 - - + +
167G VAL* 3.8 28.0 - - + -
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Residues in contact with TYR 93 (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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28F TRP 3.1 19.1 - - - +
29F ILE* 4.1 5.2 - - + -
30F ILE* 3.9 9.0 - - - +
91F MET* 3.6 15.5 - - + -
92F LEU* 1.3 76.2 - - - +
94F TYR* 1.3 78.5 + - - +
95F ASP* 5.0 0.7 - - + -
99F ASN 3.3 1.0 - - - +
100F ILE* 3.7 1.9 - - - -
101F ILE* 2.8 62.4 + - + +
103F LYS* 3.4 50.7 + - + +
105F ILE* 4.2 6.3 - - + -
61H LEU* 3.6 54.6 + - + -
63H LEU* 4.6 8.7 - - + -
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Residues in contact with TYR 94 (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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27F ASP 3.5 24.0 - - - -
28F TRP* 2.9 18.5 + - + +
30F ILE* 3.3 36.5 - - + +
93F TYR* 1.3 86.0 - - - +
95F ASP* 1.3 63.9 + - - +
98F GLN* 3.7 35.0 - - - +
99F ASN 3.4 5.2 - - - -
100F ILE* 4.3 2.0 - - + +
199G ARG* 3.0 59.5 + - + +
202G THR* 4.3 16.6 - - + -
203G CYS* 3.4 17.3 - - - +
61H LEU* 4.9 1.2 - - - +
63H LEU* 3.6 9.5 - - - +
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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