Contacts of the strand formed by residues 102 - 109 (chain A) in PDB entry 5HK1
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 GLU 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A SER 4.9 0.3 - - - +
35A PHE* 3.3 29.8 - - + +
36A VAL* 2.9 29.4 + - - +
37A PHE* 3.3 19.8 + - - -
97A HIS* 4.0 11.5 + - + +
98A ALA* 3.5 0.2 - - - -
99A SER* 2.8 40.7 + - - +
101A SER* 1.3 88.0 + - - +
103A TYR* 1.3 62.7 + - - +
173A TYR* 2.3 38.5 + - + +
174A GLY 3.3 6.5 - - - +
175A ARG* 3.9 3.1 - - - -
178A ILE* 3.7 4.2 - - - +
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Residues in contact with TYR 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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95A LEU* 4.4 6.3 - - + -
97A HIS* 3.1 15.5 - - - +
98A ALA* 4.3 5.2 - - + -
102A GLU* 1.3 77.0 - - - +
104A VAL* 1.3 66.2 + - - +
105A LEU* 3.4 35.4 - - + -
124A ILE* 3.3 21.5 - - + +
172A GLU* 2.4 37.4 + - + -
173A TYR* 3.4 8.4 - - - -
174A GLY* 3.0 49.6 + - - -
178A ILE* 3.6 34.3 - - + -
181A THR* 5.0 6.8 - - + +
301A 61W 4.0 22.6 - + + -
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Residues in contact with VAL 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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37A PHE* 3.9 26.2 - - + -
42A ILE* 4.2 12.1 - - + -
65A LEU* 4.1 15.0 - - + -
95A LEU* 3.9 0.7 - - - +
96A LEU* 2.8 45.3 + - + +
97A HIS* 2.8 22.2 + - + +
103A TYR* 1.3 80.5 - - - +
105A LEU* 1.3 64.4 + - - +
171A VAL* 4.4 13.5 - - + -
172A GLU 3.3 8.3 - - - +
173A TYR* 3.6 21.1 - - + -
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Residues in contact with LEU 105 (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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93A MET* 3.5 32.1 - - + -
94A CYS 3.3 13.0 - - - +
95A LEU* 4.1 2.9 - - + -
96A LEU* 4.3 1.3 - - - +
103A TYR* 3.4 32.3 - - + -
104A VAL* 1.3 77.6 - - - +
106A LEU* 1.3 66.4 + - - +
107A PHE* 3.6 25.4 - - + -
171A VAL* 3.6 3.1 - - - +
172A GLU* 2.8 54.4 + - + -
301A 61W 3.5 24.7 - - + +
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Residues in contact with LEU 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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58A PHE* 3.5 49.6 - - + -
61A LEU* 4.2 8.7 - - + -
62A ILE* 4.3 20.0 - - + -
81A TRP* 3.5 21.7 - - + -
93A MET* 3.0 6.6 - - - +
94A CYS* 2.8 40.8 + - + +
96A LEU* 3.9 22.9 - - + -
105A LEU* 1.3 74.3 - - - +
107A PHE* 1.3 60.0 - - - +
170A MET 3.6 2.9 - - - -
171A VAL* 3.9 23.1 - - + -
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Residues in contact with PHE 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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58A PHE* 4.8 0.2 - - - -
84A VAL* 4.4 4.9 - - + -
89A TRP* 3.6 30.5 - + - -
91A GLY* 3.7 28.3 - - - -
92A ALA 3.2 24.9 - - - -
93A MET* 4.2 7.6 - - + -
105A LEU* 3.6 15.7 + - + -
106A LEU* 1.3 74.4 - - - +
108A GLY* 1.3 74.5 + - - +
109A THR* 5.4 0.2 - - + -
164A TRP* 3.6 32.1 - + - -
169A TRP* 3.4 10.3 - - - -
170A MET* 2.8 54.1 + - + +
172A GLU* 4.7 0.7 - - - +
301A 61W 3.6 30.5 - - + -
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Residues in contact with GLY 108 (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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91A GLY* 3.2 4.9 - - - -
92A ALA 2.8 34.7 + - - +
107A PHE* 1.3 89.9 - - - +
109A THR* 1.3 62.2 + - - -
168A THR 3.1 13.7 - - - -
169A TRP* 3.3 14.4 - - - -
170A MET* 5.2 1.6 - - - -
136B TRP* 3.4 2.3 - - - -
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Residues in contact with THR 109 (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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90A MET 3.8 18.3 + - - +
91A GLY* 5.0 0.7 - - - -
107A PHE* 5.4 0.4 - - + -
108A GLY* 1.3 76.5 - - - -
110A ALA* 1.3 59.9 + - - +
111A LEU* 3.1 3.8 + - - +
112A GLY* 2.8 40.9 + - - -
113A SER 4.5 0.4 - - - +
164A TRP* 3.8 28.9 - - + -
165A GLY 4.5 1.8 - - - +
167A ASN* 3.3 4.0 + - - -
168A THR 3.0 32.6 + - - +
169A TRP* 4.0 6.6 + - - -
136B TRP* 3.5 14.4 - - - -
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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