Contacts of the strand formed by residues 79 - 84 (chain B) in PDB entry 4CFE
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 PRO 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.1 18.4 - - + -
14A GLY 6.1 1.1 - - - +
83A ILE* 4.6 9.4 - - + -
84A SER 4.4 5.2 - - - +
85A THR* 3.8 20.3 - - + +
86A PRO* 3.4 8.8 - - - +
78B ARG* 1.3 89.3 - - - +
80B THR* 1.3 58.9 + - - +
81B VAL 4.3 0.4 - - - -
115B ILE* 3.8 18.8 - - + -
116B LEU 3.2 8.1 - - - +
117B ASP* 4.2 3.5 - - - +
160B PHE* 3.4 24.1 - - + -
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PRO* 4.2 13.1 - - + +
87A THR* 6.3 0.2 - - + -
78B ARG 4.0 3.1 + - - -
79B PRO* 1.3 76.8 + - - +
81B VAL* 1.3 65.9 + - - +
82B PHE* 3.6 25.7 - - + -
115B ILE* 3.4 1.8 - - - +
116B LEU 2.6 38.9 + - - -
118B LEU* 3.6 29.8 - - + +
153B ILE* 3.8 25.8 - - + -
155B VAL* 3.8 14.6 - - + +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A THR* 4.2 15.7 - - + +
86A PRO* 5.1 0.6 - - - +
87A THR* 3.5 28.2 + - - +
88A ASP* 4.0 12.6 - - - +
90A PHE* 3.9 31.2 - - + -
80B THR* 1.3 75.1 - - - +
82B PHE* 1.3 67.2 + - - +
83B ARG* 3.9 10.7 + - + +
113B VAL* 3.7 25.6 - - + -
114B ALA 3.9 2.7 - - - -
115B ILE* 3.9 22.0 - - + -
153B ILE* 5.0 2.3 - - - +
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B THR* 3.6 31.2 - - + -
81B VAL* 1.3 72.8 - - - +
83B ARG* 1.3 58.5 + - - +
84B TRP 4.1 0.2 - - - -
93B LEU* 3.7 28.3 - - + -
97B PHE* 4.4 9.6 - + - -
105B LEU* 4.6 2.0 - - + +
112B PHE 3.7 1.6 - - - +
113B VAL* 3.2 4.9 - - - -
114B ALA* 2.9 45.8 + - + +
116B LEU* 3.9 16.4 - - + -
118B LEU* 3.6 26.9 - - + -
123B HIS* 5.6 0.4 - - + -
125B TYR* 3.4 56.1 - + + -
127B PHE* 4.7 7.6 - - + -
153B ILE* 4.2 11.4 - - + -
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS* 5.8 3.4 - - - +
48A ASN* 2.9 31.1 + - - +
88A ASP* 4.4 8.3 + - - +
81B VAL* 3.9 11.9 + - + +
82B PHE* 1.3 73.0 - - - +
84B TRP* 1.3 64.2 + - - +
85B THR* 3.5 18.3 + - - +
111B ASN* 2.9 32.3 + - - +
112B PHE 3.6 3.6 - - - +
113B VAL* 3.8 16.8 - - + -
127B PHE* 4.3 9.5 - - - -
136B ASP* 4.6 8.1 - - - +
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Residues in contact with TRP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ARG* 1.3 72.1 - - - +
85B THR* 1.3 60.2 + - - +
86B GLY* 3.1 33.8 + - - -
87B GLY 2.9 24.3 + - - -
91B VAL* 3.6 24.9 - - + +
110B ASN 3.8 1.0 - - - +
111B ASN* 3.8 4.5 - - - +
112B PHE* 2.7 48.9 + + + +
127B PHE* 3.5 46.8 - + + -
129B VAL* 3.7 17.7 - - + -
134B THR* 3.8 25.4 - - + -
135B HIS 4.0 16.8 - - - -
136B ASP* 4.6 10.3 - - - -
137B PRO* 5.5 3.4 - - + -
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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