Contacts of the strand formed by residues 79 - 84 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C LYS 5.3 0.4 - - - +
13C ILE* 3.7 25.8 - - + -
14C GLY 5.6 3.1 - - - +
83C ILE* 4.3 12.1 - - + -
84C SER 4.9 0.4 - - - +
85C THR* 3.9 15.0 - - + +
86C PRO* 3.7 7.8 - - - +
78D ARG* 1.3 88.3 - - - +
80D THR* 1.3 62.0 + - - +
115D ILE* 3.7 20.2 - - + -
116D LEU 3.2 7.4 - - - +
117D ASP* 4.2 4.0 - - - +
160D PHE* 3.3 24.4 - - + -
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Residues in contact with THR 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C PRO* 4.3 15.7 - - + +
87C THR* 5.9 0.2 - - - +
78D ARG 4.0 2.6 + - - -
79D PRO* 1.3 78.9 + - - +
81D VAL* 1.3 67.4 + - - +
82D PHE* 3.6 24.3 - - + -
115D ILE* 3.4 4.7 - - - +
116D LEU 2.7 32.7 + - - -
118D LEU* 3.7 26.3 + - + +
153D ILE* 3.7 30.1 - - + -
155D VAL* 4.1 10.6 - - + +
160D PHE* 4.7 0.2 - - - -
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Residues in contact with VAL 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C THR* 4.2 12.8 - - + +
86C PRO* 5.3 0.2 - - - +
87C THR* 3.6 25.6 + - - +
88C ASP* 3.8 14.6 - - - +
90C PHE* 3.6 37.9 - - + -
80D THR* 1.3 77.2 - - - +
82D PHE* 1.3 68.6 + - - +
83D ARG* 4.0 11.1 + - + +
113D VAL* 3.7 22.9 - - + -
114D ALA 4.2 2.2 - - - -
115D ILE* 4.1 13.7 - - + -
153D ILE* 4.9 3.1 - - - +
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Residues in contact with PHE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D THR* 3.6 26.5 - - + -
81D VAL* 1.3 72.9 - - - +
83D ARG* 1.3 60.1 + - - +
93D LEU* 3.7 26.7 - - + -
97D PHE* 4.3 11.0 - + - -
105D LEU* 4.7 3.2 - - + +
112D PHE 3.7 1.6 - - - +
113D VAL* 3.2 5.8 - - - -
114D ALA* 3.0 41.0 + - - +
116D LEU* 4.1 15.3 - - + -
118D LEU* 3.6 31.6 - - + -
123D HIS* 5.8 0.9 - - + -
125D TYR* 3.6 54.7 - + + -
127D PHE* 4.8 6.5 - - + -
153D ILE* 4.4 11.0 - - + -
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Residues in contact with ARG 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ASN* 3.4 30.7 - - - +
88C ASP* 4.3 13.5 + - - -
81D VAL* 3.9 9.8 + - + -
82D PHE* 1.3 72.7 - - - +
84D TRP* 1.3 62.7 + - - +
85D THR* 3.9 18.2 + - - +
111D ASN* 3.0 32.6 + - + +
112D PHE 3.5 2.7 - - - +
113D VAL* 3.7 22.9 - - + -
127D PHE* 4.1 11.5 - - - -
136D ASP* 4.6 8.0 - - - +
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Residues in contact with TRP 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ARG* 1.3 74.6 - - - +
85D THR* 1.3 59.7 + - - +
86D GLY* 3.0 44.2 + - - -
87D GLY 3.1 14.1 + - - -
91D VAL* 3.7 23.0 - - + +
110D ASN 3.8 4.9 - - - +
111D ASN* 3.9 2.4 - - - -
112D PHE* 2.7 47.7 + + + +
127D PHE* 3.5 51.1 - + + -
129D VAL* 3.5 18.8 - - + -
134D THR* 3.6 24.9 - - + -
135D HIS 4.1 17.3 - - - -
136D ASP* 4.4 10.8 - - - -
137D PRO* 5.7 1.8 - - + -
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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