Contacts of the strand formed by residues 83 - 92 (chain B) in PDB entry 3HQL
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 TYR 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B SO4 4.4 7.2 - - - -
73B PRO 3.8 1.6 - - - +
74B LYS* 3.7 2.1 - - - -
75B GLY* 3.0 26.5 + - - -
79B GLU 4.8 3.8 - - - -
80B SER* 3.0 15.3 + - - +
81B LYS 3.2 1.0 - - - -
82B ASP* 1.3 95.6 - - + +
84B LEU* 1.3 66.6 + - - +
134B LYS 4.0 3.1 - - - +
135B LYS* 3.7 55.9 - - + +
137B ILE 3.4 19.7 - - - +
138B ARG* 3.1 50.3 + - + -
139B ARG* 3.9 6.7 - - - -
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.8 24.5 - - + -
71B VAL* 4.0 21.1 - - + -
72B ASN 3.4 4.9 - - - +
73B PRO* 3.6 18.4 - - + +
83B TYR* 1.3 71.6 - - - +
85B SER* 1.3 60.3 + - - +
106B ILE* 6.3 0.4 - - + -
134B LYS 3.6 0.9 - - - +
136B PHE* 2.9 37.2 + - + +
137B ILE* 2.9 26.0 + - + +
139B ARG* 3.8 15.3 - - + +
142B LEU* 3.6 33.9 - - + -
143B LEU* 6.3 0.7 - - + -
155B LEU* 3.8 13.2 - - + -
157B LEU* 5.6 3.1 - - + -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ARG 3.9 0.2 - - - +
71B VAL* 3.2 8.3 - - - +
72B ASN* 2.9 42.9 + - - -
75B GLY* 3.4 3.6 - - - -
76B LEU* 3.1 24.8 + - - +
80B SER* 3.9 0.5 + - - -
84B LEU* 1.3 73.0 - - - +
86B LEU* 1.3 59.8 + - - +
87B TYR* 3.7 23.6 - - - -
133B PHE 3.4 5.6 - - - -
134B LYS* 2.6 23.9 + - - -
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TRP* 4.5 5.8 - - + -
69B LEU* 4.6 10.1 - - + -
70B ARG 3.5 18.8 - - - +
71B VAL* 4.3 7.9 - - + -
84B LEU 4.2 0.2 + - - -
85B SER* 1.3 74.4 - - - +
87B TYR* 1.3 67.4 + - - +
104B PHE* 3.5 37.1 - - + -
132B GLY* 3.4 1.9 - - - -
133B PHE 2.8 35.4 + - - -
136B PHE* 3.6 41.1 - - + -
157B LEU* 4.1 32.5 - - + -
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Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 3.4 7.8 - - - +
70B ARG* 3.0 65.4 + - + +
72B ASN* 4.5 5.2 - - - -
76B LEU* 3.4 22.7 - - + +
85B SER* 3.7 21.1 - - - -
86B LEU* 1.3 78.6 - - - +
88B LEU* 1.3 59.8 + - - +
104B PHE* 4.0 6.5 - - - -
130B ASP* 3.8 18.8 - - + -
131B TRP 3.5 6.5 - - - +
132B GLY* 3.4 28.5 - - - -
134B LYS* 3.5 26.4 - - - +
99D THR* 3.7 22.2 + - - -
101D THR* 3.6 22.4 + - + -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B PHE* 3.9 23.8 - - + -
67B TRP* 3.7 27.8 - - + -
68B CYS 3.7 14.6 - - - +
69B LEU* 3.9 8.5 - - + -
87B TYR* 1.3 73.2 - - - +
89B LEU* 1.3 60.2 + - - +
100B ALA* 5.4 0.2 - - + -
102B PHE* 3.8 19.7 - - + -
104B PHE* 3.7 15.0 - - + -
125B PHE* 3.4 22.2 - - + -
130B ASP* 3.1 5.2 - - - -
131B TRP 2.8 31.5 + - - +
159B CYS* 4.2 4.5 - - - -
161B VAL* 3.7 26.0 - - + -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LYS* 6.2 1.8 - - + -
67B TRP* 3.2 10.9 - - - +
68B CYS* 2.8 65.3 + - - +
70B ARG* 4.9 16.4 - - + -
87B TYR 4.0 0.2 - - - -
88B LEU* 1.3 75.0 - - - +
90B LEU* 1.3 66.2 + - - +
91B VAL* 3.5 9.1 + - + -
128B GLY* 3.6 26.7 - - - +
129B LYS 3.5 19.1 - - - +
130B ASP* 4.1 11.9 - - + +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU* 4.2 6.7 - - + -
66B LYS 3.6 9.4 - - - +
67B TRP* 3.9 36.0 - - + -
89B LEU* 1.3 71.3 - - - +
91B VAL* 1.3 54.9 + - - +
92B SER 3.4 22.2 - - - +
93B CYS* 3.6 26.5 - - + -
98B VAL* 3.6 13.9 - - + -
125B PHE* 3.6 29.5 - - + -
126B VAL 3.7 20.6 - - - +
127B GLN* 4.4 0.7 - - - -
128B GLY* 2.7 35.5 + - - -
129B LYS 3.0 8.1 + - - -
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B THR* 4.4 15.5 - - + -
66B LYS* 2.8 20.2 + - + +
67B TRP 4.1 1.1 - - - -
68B CYS* 3.8 41.3 - - + +
89B LEU* 3.5 11.6 + - + -
90B LEU* 1.3 74.3 - - - +
92B SER* 1.3 67.4 + - - +
127B GLN* 3.4 19.0 + - - +
128B GLY* 4.4 2.1 + - - +
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LYS 4.4 6.5 - - - -
65B LEU* 3.4 5.2 - - - -
66B LYS* 3.0 42.3 + - - +
90B LEU* 3.4 5.3 - - - +
91B VAL* 1.3 88.1 + - - +
93B CYS* 1.3 65.9 + - - +
127B GLN* 3.5 8.5 + - - -
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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