Contacts of the strand formed by residues 96 - 103 (chain A) in PDB entry 5D9L
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 LEU 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LEU* 4.3 14.1 - - + -
84A LEU* 4.0 13.5 - - + -
85A VAL 3.3 14.8 - - - +
86A LYS* 3.9 31.2 - - + +
94A ARG 3.6 2.4 + - - +
95A GLN* 1.3 95.9 + - - +
97A TYR* 1.3 65.5 + - - +
149A PHE* 4.0 32.9 + - + +
151A ARG* 3.5 28.3 - - - +
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Residues in contact with TYR 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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50A ILE* 4.9 4.9 - - - +
68A PHE* 4.5 4.3 - + - -
84A LEU* 3.5 7.1 - - - +
85A VAL* 2.9 37.5 + - + +
87A LYS* 4.0 12.8 - - + -
92A ASP* 2.6 37.3 + - - +
95A GLN* 3.5 42.4 - - + +
96A LEU* 1.3 74.1 - - - +
98A ALA* 1.3 59.8 + - - +
134A HIS* 3.5 42.3 + + - -
135A TYR* 4.1 7.4 - + - -
146A ILE* 3.5 24.2 - - + -
147A LEU 3.4 16.2 - - - +
148A ASP* 4.6 4.7 - - - -
149A PHE* 3.7 10.3 - - - +
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Residues in contact with ALA 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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74A LEU* 4.6 3.8 - - + -
82A VAL* 4.1 6.7 - - + -
83A PHE 3.4 5.8 - - - -
97A TYR* 1.3 71.5 - - - +
99A MET* 1.3 59.8 + - - +
100A LYS 4.0 0.6 + - - -
145A LEU 3.6 1.0 - - - +
146A ILE* 3.5 2.1 - - - -
147A LEU* 2.8 34.5 + - + +
148A ASP 3.4 20.2 - - - +
149A PHE* 3.8 4.6 - - + +
1001A 583 3.5 36.8 - - + +
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Residues in contact with MET 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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68A PHE* 5.2 4.3 - - - -
70A LEU* 3.8 30.5 - - + -
81A LYS 3.6 0.9 - - - +
82A VAL* 3.3 3.8 - - - -
83A PHE* 2.8 65.2 + - + +
85A VAL* 3.6 24.9 - - + -
97A TYR 4.0 0.8 + - - -
98A ALA* 1.3 72.8 - - - +
100A LYS* 1.3 62.7 + - - +
101A VAL* 3.9 13.8 + - + -
137A PHE* 4.2 9.6 - - - -
144A TYR* 3.9 22.9 - - + -
145A LEU 3.3 4.0 - - - +
146A ILE* 3.9 26.0 - - + +
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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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79A PHE* 4.5 8.7 - - + +
81A LYS 3.4 7.6 - - - +
82A VAL* 4.2 16.8 - - + +
98A ALA 4.0 1.4 - - - -
99A MET* 1.3 72.3 - - - +
101A VAL* 1.3 64.2 + - - +
102A LEU* 3.8 33.8 - - + +
118A GLU* 5.4 5.1 - - - +
143A LEU 3.7 1.6 - - - +
144A TYR* 3.5 3.6 - - - -
145A LEU* 2.8 47.4 + - + +
147A LEU* 4.3 10.3 - - + -
211A ASP* 2.8 27.2 + - - -
212A PHE* 3.3 29.3 - - + +
1001A 583 2.9 25.3 + - + -
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Residues in contact with VAL 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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80A GLY* 3.6 7.6 - - - -
81A LYS* 2.8 35.7 + - + +
83A PHE* 3.6 37.9 - - + -
99A MET* 4.1 5.2 - - + +
100A LYS* 1.3 76.7 - - - +
102A LEU* 1.3 62.2 + - - +
103A LYS 4.4 0.3 + - - -
142A LYS* 3.6 37.7 - - + +
143A LEU 3.4 2.0 - - - +
144A TYR* 3.7 30.3 - - + -
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Residues in contact with LEU 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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79A PHE* 3.2 29.6 - - + +
80A GLY* 5.2 0.2 - - - -
100A LYS* 3.8 24.2 - - + +
101A VAL* 1.3 75.9 - - - +
103A LYS* 1.3 66.1 + - - +
106A THR* 5.1 4.0 - - - +
107A LEU* 4.9 7.9 - - + -
118A GLU* 3.7 38.1 - - + +
142A LYS* 3.3 7.9 - - - -
143A LEU* 2.8 57.9 + - + +
145A LEU* 3.8 20.6 - - + -
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Residues in contact with LYS 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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79A PHE 5.7 0.2 + - - -
81A LYS* 6.5 0.9 - - - +
101A VAL* 4.4 1.0 + - + +
102A LEU* 1.3 71.8 - - - +
104A LYS* 1.3 62.2 + - - +
105A ALA* 3.2 7.6 - - + +
106A THR* 2.7 45.8 + - + +
107A LEU* 4.0 3.3 + - - +
141A GLY 3.8 6.3 - - - +
142A LYS* 3.9 27.6 - - + +
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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