Contacts of the strand formed by residues 101 - 109 (chain A) in PDB entry 2YD0
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 GLN 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A LEU* 1.3 69.7 - - - +
102A ILE* 1.3 67.7 + - - +
103A SER* 3.8 1.4 + - - -
151A TYR* 3.2 4.2 - - - -
152A ALA* 2.9 41.9 + - + +
1C NAG 3.9 14.5 - - + +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A SER* 4.0 20.4 - - - +
100A LEU* 3.7 10.7 + - + +
101A GLN* 1.3 79.1 - - - +
103A SER* 1.3 62.8 + - - +
104A ARG 3.9 10.8 - - - +
105A ALA* 4.9 1.1 - - + -
122A VAL* 4.3 29.5 - - + +
131A ILE* 4.6 22.4 - - + -
133A LEU* 5.9 0.4 - - + -
149A ILE* 3.8 29.4 - - + -
150A HIS 3.7 3.4 - - - +
151A TYR* 3.7 19.5 - - + -
192A PRO* 4.8 3.8 - - + -
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLN 3.8 2.0 + - - -
102A ILE* 1.3 74.4 - - - +
104A ARG* 1.3 63.2 + - - +
122A VAL* 6.2 0.7 - - - -
150A HIS* 3.0 24.1 + - - +
151A TYR* 4.2 4.9 + - - -
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 3.6 4.4 - - - +
103A SER* 1.3 82.8 - - - +
105A ALA* 1.3 65.4 + - - +
106A THR* 3.4 30.3 - - + +
117A GLU* 4.1 13.1 + - - -
119A PRO* 4.4 15.6 - - - +
122A VAL* 5.6 2.2 - - - +
148A VAL 3.8 0.6 - - - +
149A ILE* 3.4 5.0 - - - +
150A HIS* 3.0 55.2 + - + +
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 4.9 2.0 - - + -
104A ARG* 1.3 77.9 + - - +
106A THR* 1.3 67.5 + - - +
119A PRO* 3.8 1.7 - - - +
120A LEU* 2.9 36.0 + - + +
122A VAL* 3.9 15.1 - - + +
133A LEU* 3.8 29.4 - - + -
147A VAL* 5.7 0.2 - - + -
148A VAL 3.2 7.9 - - - +
149A ILE* 4.4 8.3 - - + -
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Residues in contact with THR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG* 3.4 42.6 - - + +
105A ALA* 1.3 80.4 - - - +
107A LEU* 1.3 62.0 + - - +
108A ARG* 4.7 0.2 + - - -
117A GLU* 3.3 28.2 + - - +
118A GLU 3.2 14.6 - - - +
119A PRO* 4.2 3.4 - - + -
120A LEU* 3.7 8.6 - - - +
146A THR 3.8 0.3 - - - +
147A VAL* 3.4 4.2 - - - -
148A VAL* 2.9 49.9 + - - +
150A HIS* 5.9 1.8 + - + -
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 4.8 0.2 - - + -
93A ILE* 4.5 10.5 - - + -
106A THR* 1.3 74.2 - - - +
108A ARG* 1.3 61.9 + - - +
116A SER 3.9 0.7 - - - +
117A GLU* 3.5 4.1 - - - -
118A GLU* 2.8 39.6 + - + +
120A LEU* 3.9 14.3 - - + +
135A ALA* 4.2 25.4 - - + -
136A PRO* 5.5 2.7 - - + -
137A GLU* 5.2 5.2 - - - +
138A PRO 6.3 0.2 - - - -
139A LEU* 4.2 10.5 - - + -
145A TYR* 3.8 42.8 - - + -
146A THR 3.5 3.1 - - - +
147A VAL* 3.8 25.8 - - + -
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LYS* 4.5 20.2 - - - +
106A THR 4.2 0.2 - - - -
107A LEU* 1.3 76.3 - - - +
109A LYS* 1.3 61.2 - - - +
110A GLY 3.7 2.4 + - - +
115A LEU 5.8 4.5 - - - +
116A SER 3.5 6.5 - - - +
117A GLU* 3.1 36.7 + - + -
145A TYR* 3.3 12.5 - - - +
146A THR* 2.8 46.9 + - - +
148A VAL* 3.8 33.6 - - + +
150A HIS* 6.1 0.2 + - - -
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU 4.2 0.2 + - - -
108A ARG* 1.3 70.5 - - - +
110A GLY* 1.3 56.0 + - - +
115A LEU* 3.9 20.0 + - - +
116A SER* 3.2 28.0 + - - +
144A PRO 4.3 0.4 - - - -
145A TYR* 4.3 20.2 - - + -
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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