Contacts of the strand formed by residues 99 - 104 (chain D) in PDB entry 3EGC
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 SER 99 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LEU* 3.7 19.2 - - - +
118C GLN* 3.6 22.9 + - - +
119C PHE* 4.5 2.1 - - - -
122C ARG* 3.0 34.6 + - - +
68D ASN 2.8 9.9 + - - -
69D VAL* 3.4 3.9 - - - -
70D VAL* 2.9 27.1 + - - +
97D GLY 4.2 0.2 + - - -
98D TYR* 1.3 75.3 - - - +
100D VAL* 1.3 65.8 + - - +
101D LEU 4.2 0.4 - - - -
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Residues in contact with VAL 100 (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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101C LEU* 3.2 8.5 - - - +
102C LEU* 2.7 52.7 + - + +
119C PHE* 5.8 0.8 - - - -
70D VAL* 3.5 5.8 - - + +
72D LEU* 3.8 28.7 - - + -
89D VAL* 4.7 4.0 - - + -
90D GLU* 4.4 16.6 - - + -
93D ALA* 3.6 26.9 - - + -
98D TYR 4.7 0.2 - - - +
99D SER* 1.3 82.0 - - - +
101D LEU* 1.3 71.1 + - - +
102D LEU* 4.8 0.4 - - - +
308D MET* 4.1 11.7 - - + -
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Residues in contact with LEU 101 (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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69C VAL* 4.3 7.6 - - + -
99C SER* 3.7 22.0 - - - -
100C VAL 3.3 15.0 - - - +
101C LEU* 3.7 19.7 - - + +
69D VAL* 3.9 14.6 - - + +
70D VAL 2.9 12.0 + - - +
71D GLY* 3.7 0.8 - - - -
72D LEU* 2.7 33.3 + - - +
99D SER 4.2 0.2 - - - -
100D VAL* 1.3 76.4 - - - +
102D LEU* 1.3 57.0 + - - +
119D PHE* 3.8 28.2 - - + -
122D ARG* 3.9 21.8 - - + -
124D VAL* 3.8 24.0 - - + -
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Residues in contact with LEU 102 (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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72C LEU* 5.1 1.3 - - + -
77C ILE* 6.0 0.7 - - + -
86C ALA* 5.0 13.5 - - + +
90C GLU* 3.8 24.4 - - + +
100C VAL* 2.7 34.6 + - + +
102C LEU* 4.1 37.0 - - + -
72D LEU* 3.5 25.1 - - + +
74D VAL* 4.9 2.7 - - + -
77D ILE* 4.4 31.4 - - + -
100D VAL* 5.4 0.9 - - + -
101D LEU* 1.3 74.9 - - - +
103D ALA* 1.3 81.5 + - - +
104D ASN* 5.6 0.4 - - + -
119D PHE* 3.7 6.4 - - - -
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Residues in contact with ALA 103 (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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90C GLU* 3.4 11.2 - - - +
94C ARG* 5.2 3.4 - - - -
72D LEU 2.8 9.5 + - - +
73D ILE* 4.3 4.9 - - + -
74D VAL* 3.0 25.3 + - - +
102D LEU* 1.3 83.5 - - - +
104D ASN* 1.3 63.0 + - - +
115D ALA* 3.8 25.1 - - + -
118D GLN* 5.6 2.2 - - - +
119D PHE* 3.6 21.3 - - + -
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Residues in contact with ASN 104 (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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87C SER* 3.5 23.0 + - - -
90C GLU* 3.0 27.8 + - + +
94C ARG* 3.1 10.7 + - - -
74D VAL* 3.6 3.2 - - - +
76D ASP* 3.4 15.1 + - - -
77D ILE* 2.9 47.0 + - + +
78D GLU* 4.8 2.8 + - - -
102D LEU* 5.5 1.6 - - + -
103D ALA* 1.3 74.8 - - - +
105D THR* 1.3 62.1 + - - +
106D ALA* 3.6 12.6 + - - +
111D ARG* 3.0 22.1 + - - +
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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