Contacts of the strand formed by residues 93 - 101 (chain D) in PDB entry 3B94
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 GLY 93 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ASN* 1.3 78.8 - - - +
94D LEU* 1.3 61.3 + - - -
95D TYR* 3.4 12.8 - - - -
141D GLU* 3.4 4.6 - - - +
142D LEU 3.0 30.8 + - - -
169D LEU* 3.9 1.8 - - - -
171D ALA 3.1 12.1 - - - -
172D ASN* 4.1 5.2 - - - -
173D PRO* 5.2 2.9 - - - -
175D PHE 5.6 2.8 + - - -
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Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D GLY* 1.3 72.6 - - - -
95D TYR* 1.3 53.1 + - - +
139D THR* 3.8 18.4 - - + -
140D TYR* 3.4 20.4 - - - +
141D GLU* 4.0 7.9 - - + +
169D LEU* 3.6 2.6 - - - +
170D LEU* 2.6 64.7 + - + -
171D ALA* 2.6 26.0 + - + +
173D PRO* 5.0 6.4 - - + +
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Residues in contact with TYR 95 (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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78D CYS* 3.5 35.3 + - - +
79D VAL* 4.6 6.1 - - + -
89D ILE* 4.2 6.5 - - + -
91D GLN* 2.7 32.5 + - - +
93D GLY 3.4 26.0 - - - -
94D LEU* 1.3 75.1 - - - +
96D LEU* 1.3 60.1 + - - +
97D ILE* 3.9 1.9 + - + -
138D GLY 3.9 0.5 - - - +
139D THR* 3.1 8.3 - - - +
140D TYR* 2.7 38.3 + - - +
142D LEU* 3.7 31.6 - - + -
167D ILE* 3.7 31.9 - - + -
168D ILE 3.3 11.9 - - - +
169D LEU* 3.5 26.8 - - + +
170D LEU* 4.6 0.7 - - - -
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Residues in contact with LEU 96 (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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95D TYR* 1.3 71.9 - - - +
97D ILE* 1.3 70.8 + - - +
98D TYR* 4.0 6.9 + - + -
138D GLY* 3.6 14.1 - - - +
139D THR* 3.6 18.8 - - - +
167D ILE* 3.2 3.2 - - - +
168D ILE* 2.9 49.7 + - + +
170D LEU* 4.2 27.3 - - + +
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Residues in contact with ILE 97 (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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95D TYR 5.0 1.8 - - - +
96D LEU* 1.3 81.8 - - - +
98D TYR* 1.4 68.4 + - - +
117D LEU* 4.0 25.8 - - + -
124D ILE* 4.4 1.8 - - + -
136D VAL* 4.7 1.6 - - + +
137D GLY* 3.1 9.8 - - - -
138D GLY 2.9 34.1 + - - +
140D TYR* 4.2 19.7 - - + -
142D LEU* 4.7 3.8 - - + -
148D ILE* 3.8 39.9 - - + -
165D TRP* 3.8 17.3 - - + -
166D GLY 3.4 11.9 - - - +
167D ILE* 3.9 17.7 - - + -
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Residues in contact with TYR 98 (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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59D MET* 4.1 22.3 - - + +
60D ALA 4.2 2.4 + - - -
61D LYS* 4.2 15.5 - - + +
96D LEU* 4.4 12.6 - - + -
97D ILE* 1.4 77.9 - - - +
99D GLY* 1.3 63.8 + - - +
136D VAL* 3.1 13.9 - - - -
164D TYR* 4.1 22.7 - + - -
165D TRP* 3.3 4.3 - - - +
166D GLY* 2.9 63.8 + - - +
167D ILE* 3.6 8.5 - - - -
168D ILE* 5.0 6.5 - - + -
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Residues in contact with GLY 99 (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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98D TYR* 1.3 88.1 - - - +
100D GLN* 1.3 61.1 + - - +
135D ASN* 3.6 13.9 + - - -
136D VAL* 3.0 27.0 + - - +
164D TYR* 3.0 20.6 - - - -
165D TRP* 3.9 0.9 - - - -
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Residues in contact with GLN 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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99D GLY* 1.3 74.6 - - - +
101D VAL* 1.3 68.7 + - - +
102D ALA* 4.5 0.4 - - + +
133D ILE* 3.9 24.0 - - + +
134D GLN 3.3 8.3 - - - +
135D ASN* 5.1 5.0 - - - +
136D VAL* 4.2 1.8 - - - +
162D ASN* 3.3 41.3 + - - +
163D THR* 3.2 2.8 - - - +
164D TYR* 2.9 56.1 + - + +
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Residues in contact with VAL 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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100D GLN* 1.3 79.2 - - - +
102D ALA* 1.3 68.4 + - - +
103D PRO* 3.2 14.5 - - + +
115D VAL* 4.0 32.5 - - + -
127D LEU* 3.6 26.9 - - + -
133D ILE* 3.5 2.4 - - - +
134D GLN* 2.7 32.7 + - + +
136D VAL* 3.8 15.7 - - + -
150D LEU* 4.1 15.7 - - + -
152D PHE* 4.9 0.7 - - + -
158D VAL* 4.7 9.2 - - + -
163D THR* 3.9 9.2 - - + +
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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