Contacts of the strand formed by residues 98 - 107 (chain A) 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 VAL 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.9 20.4 - - + -
67A TRP* 3.9 31.0 - - + -
90A LEU* 4.0 15.9 - - + -
93A CYS* 4.7 5.1 - - - -
97A GLU* 1.3 77.4 - - - +
99A ARG* 1.3 68.7 + - - +
100A ALA* 5.0 0.4 - - + -
123A TYR 3.6 0.5 - - - +
124A ARG* 3.7 1.8 - - - -
125A PHE* 2.8 34.0 + - + +
163A VAL* 3.7 23.8 - - + -
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Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLU* 5.7 4.6 - - + +
98A VAL* 1.3 78.3 - - - +
100A ALA* 1.3 62.1 + - - +
122A ALA* 4.2 16.9 + - + -
123A TYR 3.3 9.2 - - - +
124A ARG* 4.1 36.5 - - + +
163A VAL* 3.4 27.1 - - - +
164A VAL 3.9 16.1 + - - +
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Residues in contact with ALA 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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67A TRP* 4.0 10.1 - - + -
88A LEU* 5.4 0.4 - - + -
98A VAL 4.1 0.2 + - - -
99A ARG* 1.3 75.8 - - - +
101A LYS* 1.3 58.4 + - - +
102A PHE* 4.0 3.8 - - - -
122A ALA* 3.8 7.2 - - - +
123A TYR* 2.9 29.1 + - - +
125A PHE* 3.8 22.6 - - + -
161A VAL* 4.0 21.5 - - + -
162A SER 3.3 10.1 - - - +
163A VAL* 4.0 8.5 - - + -
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Residues in contact with LYS 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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100A ALA* 1.3 74.8 - - - +
102A PHE* 1.3 64.0 + - - +
119A SER* 3.4 13.2 - - - +
120A GLN 5.0 2.8 + - - +
121A ARG* 3.7 12.1 - - - +
122A ALA* 3.4 34.9 - - + +
161A VAL* 3.4 4.9 - - - +
162A SER* 2.9 43.7 + - - +
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Residues in contact with PHE 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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88A LEU* 3.8 20.6 - - + -
100A ALA 4.0 6.7 - - - -
101A LYS* 1.3 80.9 - - - +
103A LYS* 1.3 62.2 + - - +
104A PHE* 3.6 24.7 - + + -
118A GLU* 3.5 1.9 - - - +
119A SER* 2.8 48.3 + - - -
123A TYR* 4.1 11.4 - + + -
125A PHE* 4.2 15.5 - + - -
131A TRP* 3.8 33.9 - - + -
132A GLY* 4.0 10.1 - - - -
133A PHE* 3.8 28.5 - + - -
160A GLU 3.2 10.8 - - - +
161A VAL* 4.5 0.9 - - + -
98C VAL* 3.9 13.7 - - + -
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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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102A PHE* 1.3 76.8 - - - +
104A PHE* 1.3 71.4 + - - +
105A SER* 5.5 0.2 - - - -
113A GLU* 3.3 21.2 + - - +
116A ALA* 3.5 23.5 - - - +
117A MET 3.3 13.9 - - - +
118A GLU* 4.0 16.4 - - + -
158A PHE 3.8 0.5 - - - +
159A CYS* 3.4 3.8 - - - -
160A GLU* 2.9 57.7 + - + +
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Residues in contact with PHE 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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69A LEU* 4.2 5.8 - - + -
86A LEU* 3.5 49.1 - - + -
87A TYR 4.0 1.8 - - - -
88A LEU* 3.7 28.0 - - + -
102A PHE* 3.6 23.1 - + + -
103A LYS* 1.3 83.3 - - - +
105A SER* 1.3 61.1 + - - +
116A ALA* 3.1 3.5 - - - +
117A MET 2.9 32.0 + - - +
132A GLY* 4.2 3.1 - - - -
133A PHE* 3.5 30.3 - + - -
136A PHE* 3.7 15.6 - + + -
158A PHE 3.3 4.9 - - - +
159A CYS* 3.5 31.6 - - + -
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Residues in contact with SER 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LYS* 5.4 1.6 - - - -
104A PHE* 1.3 77.0 - - - +
106A ILE* 1.3 65.2 + - - +
107A LEU* 4.2 0.3 - - - +
113A GLU* 3.4 37.1 + - - +
114A THR 3.6 12.6 - - - -
116A ALA* 3.8 14.8 - - - +
136A PHE* 4.2 5.1 - - - -
157A LEU* 3.4 7.3 - - - +
158A PHE* 2.9 43.1 + - - +
160A GLU* 4.8 1.0 + - - -
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Residues in contact with ILE 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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105A SER* 1.3 76.1 - - - +
107A LEU* 1.3 73.0 + - - +
112A GLU 3.5 0.2 - - - +
113A GLU* 3.6 0.9 - - - -
114A THR* 2.8 44.0 + - + +
115A LYS* 4.3 8.1 - - + -
136A PHE* 3.9 26.2 - - + -
137A ILE* 4.3 26.2 - - + -
142A LEU* 4.4 7.4 - - + -
149A LEU* 4.1 33.2 - - + +
155A LEU* 4.0 16.4 - - + -
156A THR 3.5 10.1 - - - +
157A LEU* 3.9 8.7 - - + -
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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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35A MET* 4.0 19.3 - - + -
105A SER* 4.2 0.2 - - - +
106A ILE* 1.3 84.4 - - - +
108A ASN* 1.3 67.8 + - - +
111A GLY* 3.9 24.2 - - - +
112A GLU 3.3 2.7 - - - +
113A GLU* 3.6 33.2 - - + -
149A LEU* 4.5 7.5 - - - +
151A PRO* 5.2 2.9 - - - +
156A THR* 2.9 45.9 + - + +
158A PHE* 3.8 26.7 - - + -
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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