Contacts of the strand formed by residues 99 - 104 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C ASN 2.7 11.1 + - - -
69C VAL* 4.2 3.8 - - - -
70C VAL* 2.8 32.4 + - - +
97C GLY 4.3 0.2 + - - -
98C TYR* 1.3 76.4 - - - +
100C VAL* 1.3 62.1 + - - +
101C LEU 4.2 0.7 - - - -
101D LEU* 3.7 19.9 - - - +
118D GLN* 3.8 19.3 + - - +
119D PHE* 5.2 1.3 - - - -
122D ARG* 2.8 35.7 + - - -
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Residues in contact with VAL 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C VAL* 3.7 5.8 - - + +
72C LEU* 3.9 35.4 - - + -
89C VAL* 4.5 8.5 - - + -
90C GLU* 4.2 19.7 - - + -
93C ALA* 3.6 27.1 - - + -
98C TYR 4.7 0.4 - - - +
99C SER* 1.3 80.9 - - - +
101C LEU* 1.3 62.8 + - - +
102C LEU* 3.7 0.4 + - - -
308C MET* 4.7 2.9 - - + -
101D LEU* 3.3 6.4 - - - +
102D LEU* 2.7 55.7 + - + +
119D PHE* 5.8 1.0 - - - -
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Residues in contact with LEU 101 (chain C).
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* 3.9 14.6 - - + -
70C VAL 3.0 13.3 + - - +
71C GLY* 4.5 0.4 - - - -
72C LEU* 2.8 32.9 + - - +
99C SER 4.2 0.2 - - - -
100C VAL* 1.3 73.1 - - - +
102C LEU* 1.3 60.4 + - - +
119C PHE* 3.6 25.2 - - + -
122C ARG* 3.9 25.6 - - + -
124C VAL* 3.8 23.1 - - + -
69D VAL* 4.6 5.6 - - + -
99D SER* 3.7 19.5 - - - +
100D VAL 3.2 26.0 - - - +
101D LEU* 3.7 15.4 - - + +
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Residues in contact with LEU 102 (chain C).
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* 3.5 25.1 - - + +
74C VAL* 5.0 2.5 - - + -
77C ILE* 4.4 28.9 - - + -
100C VAL* 3.7 1.1 + - + -
101C LEU* 1.3 75.4 - - - +
103C ALA* 1.3 78.8 + - - +
104C ASN* 4.9 1.6 - - + +
119C PHE* 3.7 5.6 - - - -
72D LEU* 5.0 4.9 - - + -
77D ILE* 5.8 0.7 - - + -
86D ALA* 4.6 25.8 - - + +
90D GLU* 3.7 18.6 - - + +
100D VAL* 2.7 28.9 + - + +
102D LEU* 4.1 35.4 - - + -
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Residues in contact with ALA 103 (chain C).
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 2.9 10.6 + - - +
73C ILE* 4.2 5.4 - - + -
74C VAL* 3.1 24.8 + - - +
102C LEU* 1.3 81.5 - - - +
104C ASN* 1.3 59.8 + - - +
105C THR* 5.7 0.2 - - + -
115C ALA* 3.7 24.7 - - + -
118C GLN* 5.4 2.7 - - - +
119C PHE* 3.6 21.1 - - + -
90D GLU* 3.2 14.1 - - - +
94D ARG* 4.9 3.4 - - - +
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Residues in contact with ASN 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C VAL* 3.5 4.8 - - - +
76C ASP* 3.4 13.1 + - - +
77C ILE* 2.8 46.9 + - + +
78C GLU* 5.0 2.8 + - - -
102C LEU* 5.6 2.7 - - + -
103C ALA* 1.3 73.6 - - - +
105C THR* 1.3 61.1 + - - +
106C ALA* 3.8 13.7 + - - +
111C ARG* 2.8 24.0 + - - +
87D SER* 3.5 22.6 + - - +
90D GLU* 2.9 28.7 + - + +
94D ARG* 3.3 7.8 + - - -
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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