Contacts of the strand formed by residues 99 - 105 (chain Y) in PDB entry 3AOH
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 ARG 99 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90Y GLU* 4.1 22.1 + - + +
91Y LEU 3.7 1.8 - - - -
92Y GLU* 3.9 32.4 + - - +
97Y GLY 3.5 5.1 + - - +
98Y GLU* 1.3 77.5 + - - +
100Y LEU* 1.3 61.0 + - - +
101Y SER 4.2 1.1 + - - -
152Y VAL* 3.4 38.7 - - - +
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Residues in contact with LEU 100 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980I MET* 6.2 4.3 - - - -
89Y VAL 3.9 0.3 - - - +
90Y GLU* 3.1 7.8 - - - -
91Y LEU* 2.8 57.3 + - + +
98Y GLU* 5.2 1.6 - - + +
99Y ARG* 1.3 76.8 - - - +
101Y SER* 1.3 80.3 + - - +
102Y VAL* 4.1 6.5 + - + +
117Y MET* 4.9 15.7 - - + -
125Y MET* 5.0 19.3 - - + -
149Y PHE* 5.0 20.0 - - + -
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Residues in contact with SER 101 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Y VAL* 5.1 3.6 - - - +
89Y VAL 3.7 5.0 + - - -
90Y GLU* 4.5 11.4 - - - -
99Y ARG 4.2 1.2 + - - -
100Y LEU* 1.3 86.0 - - - +
102Y VAL* 1.3 63.1 + - - +
115Y THR 4.7 1.1 + - - -
116Y PRO* 3.6 23.4 - - - +
117Y MET* 3.6 15.5 + - - +
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Residues in contact with VAL 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982I PHE* 5.2 0.2 - - + -
88Y VAL* 3.5 5.9 - - - +
89Y VAL* 2.8 39.0 + - + +
91Y LEU* 5.9 4.7 - - + -
100Y LEU* 4.1 8.5 + - + +
101Y SER* 1.3 77.3 + - - +
103Y GLN* 1.3 68.0 + - - +
104Y VAL 4.3 0.9 - - - +
116Y PRO* 4.1 3.8 - - - -
117Y MET* 3.0 31.0 - - + +
119Y ILE* 3.0 36.3 - - + -
125Y MET* 3.3 15.3 - - + -
129Y LEU* 3.7 17.7 - - + -
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Residues in contact with GLN 103 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y THR* 4.5 10.3 + - - +
10Y ALA* 5.9 2.0 - - - +
86Y GLY 3.9 11.8 + - - +
87Y SER 3.3 19.1 - - - +
88Y VAL* 3.4 24.0 - - + +
102Y VAL* 1.3 79.0 - - - +
104Y VAL* 1.3 65.0 + - - +
105Y VAL* 3.5 16.0 + - - +
116Y PRO* 3.8 24.5 - - + +
117Y MET 3.2 5.9 + - - -
118Y LYS* 3.2 35.7 - - + +
119Y ILE 2.9 21.9 + - - -
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Residues in contact with VAL 104 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Y ILE* 4.5 9.6 - - + -
84Y GLY 4.7 8.3 - - - +
85Y LEU* 3.6 3.8 - - + +
86Y GLY* 3.1 27.5 + - - -
87Y SER 3.2 9.4 + - - +
89Y VAL* 4.9 0.4 - - + -
102Y VAL* 4.3 1.6 - - + -
103Y GLN* 1.3 72.2 - - - +
105Y VAL* 1.3 62.5 + - - +
119Y ILE* 3.4 24.7 - - + -
120Y SER 3.7 20.9 - - - +
121Y ASP* 4.0 18.8 - - - +
126Y GLY* 4.2 12.6 - - - +
129Y LEU* 3.7 26.5 - - + -
130Y LEU* 4.9 7.2 - - + -
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Residues in contact with VAL 105 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y THR* 4.1 9.4 - - + -
85Y LEU* 3.5 12.3 - - + -
86Y GLY 4.9 0.7 - - - +
103Y GLN* 4.0 20.6 - - - +
104Y VAL* 1.3 77.9 - - - +
106Y SER* 1.3 58.7 + - - +
109Y GLU* 3.1 53.8 - - + +
110Y ALA 3.9 2.0 - - - +
118Y LYS* 3.5 30.7 - - + -
119Y ILE 2.7 16.6 + - - +
120Y SER 3.1 0.3 - - - -
121Y ASP 2.6 31.9 + - - -
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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