Contacts of the strand formed by residues 94 - 101 (chain A) in PDB entry 1D02
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 ILE 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A TYR* 5.2 0.9 - - + -
48A HIS* 3.4 37.0 - - + +
85A ALA* 3.7 15.7 - - + -
86A ILE 3.4 11.2 - - - +
87A GLU* 3.8 23.8 - - + +
92A HIS 3.7 11.9 - - - +
93A LYS* 1.3 81.0 - - - +
95A LEU* 1.3 62.2 + - - +
96A PHE* 3.7 34.2 + - + -
137A ILE 4.7 8.5 - - - +
138A GLY* 2.8 28.2 + - - +
140A ILE* 3.6 10.6 - - - +
147A PRO* 4.7 1.2 - - - +
201A LEU* 3.9 4.0 - - - +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 5.1 1.9 - - + -
85A ALA* 3.2 3.5 - - - +
86A ILE* 2.8 45.6 + - + +
94A ILE* 1.3 71.5 - - - +
96A PHE* 1.3 62.0 + - - +
97A GLY 4.0 0.2 + - - -
140A ILE* 4.0 11.0 - - + -
146A LEU 4.8 3.6 - - - +
147A PRO 3.7 20.4 - - - +
148A PHE 3.9 19.7 - - - +
149A TRP* 4.1 21.5 - - + -
193A PHE* 4.2 13.2 - - + -
197A LEU* 3.9 42.2 - - + +
201A LEU* 3.8 15.8 - - + +
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Residues in contact with PHE 96 (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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46A PRO* 4.3 4.3 - - + -
48A HIS* 3.7 40.8 - + + -
49A LEU* 3.8 26.2 - - + -
82A PRO* 4.1 13.2 - - + -
84A PHE 3.8 1.3 - - - -
85A ALA* 3.7 14.8 - - + -
94A ILE* 3.7 26.0 - - + -
95A LEU* 1.3 74.2 - - - +
97A GLY* 1.3 59.7 + - - +
134A TYR* 3.4 35.9 - + + -
137A ILE* 4.1 7.6 - - + -
138A GLY* 3.9 27.8 - - - -
147A PRO* 3.6 7.4 + - + -
148A PHE* 3.1 9.6 - - - +
149A TRP* 3.0 22.0 + - - -
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Residues in contact with GLY 97 (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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82A PRO* 3.6 0.9 - - - +
83A ALA 3.0 22.5 + - - -
84A PHE* 2.7 40.0 + - - +
95A LEU 4.0 0.6 + - - -
96A PHE* 1.3 76.7 - - - +
98A GLU* 1.3 72.0 + - - +
148A PHE* 5.4 0.2 - - - -
149A TRP* 3.1 11.7 - - - -
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Residues in contact with GLU 98 (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 SER 4.9 2.3 - - - +
82A PRO* 3.4 18.9 - - - +
83A ALA* 3.9 11.5 + - - +
84A PHE* 3.5 8.4 - - - -
97A GLY* 1.3 83.0 - - - +
99A ILE* 1.3 64.8 + - - +
100A LYS* 4.5 19.6 + - - -
122A SER* 5.2 5.2 - - - -
124A LYS* 6.5 0.7 - - - -
125A LEU* 3.5 29.5 - - + +
134A TYR* 3.8 12.3 + - - -
149A TRP 2.9 5.3 + - - -
150A VAL* 4.2 19.1 - - + -
151A VAL 2.9 23.6 + - - -
3D C 5.4 3.6 - - - +
4D A 4.8 5.9 + - - -
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Residues in contact with ILE 99 (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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27A LEU* 4.0 26.7 - - + -
28A TYR* 3.8 36.8 - - + +
83A ALA* 3.7 10.3 - - + +
84A PHE* 3.9 13.9 - - + -
98A GLU* 1.3 81.4 + - - +
100A LYS* 1.3 72.6 + - - +
101A ARG* 3.7 38.3 + - + +
151A VAL* 3.2 6.7 - - + +
153A GLU* 3.6 25.4 - - - +
4D A 3.7 12.6 + - - +
5D A 5.4 0.5 + - - -
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Residues in contact with LYS 100 (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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98A GLU* 4.2 16.0 + - - -
99A ILE* 1.3 83.4 - - - +
101A ARG* 1.3 61.7 + - - +
102A GLN* 4.0 0.6 + - - -
118A ALA 5.1 0.9 - - - +
119A HIS* 4.5 20.4 - - + +
121A ARG* 3.2 29.9 - - - +
122A SER* 3.9 33.3 - - - +
150A VAL* 4.1 9.6 - - + -
151A VAL 2.8 10.5 + - - +
152A PHE* 3.3 27.2 - - + -
153A GLU 2.9 23.7 + - - +
156A ILE* 4.7 1.4 - - - +
4D A 2.6 30.6 + - - -
5D A 6.2 2.2 - - + -
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Residues in contact with ARG 101 (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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26A ASN* 6.3 1.4 - - - +
28A TYR* 5.0 8.1 - - - -
99A ILE* 3.7 36.3 + - + +
100A LYS* 1.3 74.6 - - - +
102A GLN* 1.3 65.7 + - - +
153A GLU* 3.1 38.0 + - + +
154A GLY* 5.6 0.9 - - - -
4D A 4.7 9.5 + - - -
5D A 3.0 60.2 + - - +
6D T 4.8 1.6 - - - +
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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