Contacts of the strand formed by residues 108 - 115 (chain A) in PDB entry 6AL5
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 GLN 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A LEU* 3.4 7.5 - - - -
97A CYS* 2.7 61.3 + - + +
98A GLN* 4.5 0.7 - - - -
99A PRO* 4.3 20.7 - - - +
106A ALA 3.9 7.0 + - - +
107A TRP* 1.3 78.5 - - - +
109A PRO* 1.3 79.6 - - + +
110A GLY 3.1 0.5 + - - -
200A CYS* 4.8 8.9 - - - +
201A GLY* 5.6 1.9 + - - -
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Residues in contact with PRO 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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96A LEU* 4.4 3.1 - - + -
97A CYS* 4.9 1.4 - - - +
108A GLN* 1.3 89.0 - - + +
110A GLY* 1.3 63.1 + - - +
124A TRP* 3.6 46.0 - - + -
159A TRP* 5.2 7.4 - - + +
186A GLN* 3.7 18.5 + - - +
902A NAG 5.5 4.7 - - - +
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Residues in contact with GLY 110 (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 TYR 3.0 15.1 + - - -
96A LEU* 4.2 0.2 - - - +
97A CYS* 4.7 5.6 - - - -
108A GLN 3.1 5.3 + - - -
109A PRO* 1.3 70.9 - - - +
111A TRP* 1.3 76.0 + - - -
124A TRP* 4.0 2.1 + - - -
186A GLN* 2.8 34.6 + - - +
199A SER 5.1 1.3 - - - -
201A GLY 6.0 2.5 - - - -
214A TRP* 4.3 12.1 - - - -
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Residues in contact with TRP 111 (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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81A TRP* 6.2 1.3 - + - -
95A TYR* 2.7 38.9 + - + +
110A GLY* 1.3 86.2 - - - +
112A THR* 1.3 61.0 + - - +
113A VAL* 5.5 0.9 - - + -
124A TRP* 3.6 7.0 - - - +
185A SER 3.6 20.9 - - - -
186A GLN* 3.4 40.4 - - + +
188A LEU* 3.9 35.2 - - + -
197A TRP 5.8 0.4 - - - -
198A LEU* 3.4 37.5 - - + +
199A SER* 3.5 35.6 + - - +
201A GLY 5.0 5.1 - - - +
202A VAL* 4.8 14.4 - - + -
214A TRP* 4.0 4.0 - + - -
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Residues in contact with THR 112 (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 GLY 3.2 7.9 - - - -
94A PHE* 3.5 28.3 - - + -
111A TRP* 1.3 75.8 - - - +
113A VAL* 1.3 62.5 + - - +
114A ASN* 3.3 2.9 + - - -
122A PHE* 3.2 21.3 + - - +
124A TRP* 3.3 24.5 - - + +
186A GLN 3.1 4.8 + - - -
187A ASP* 2.6 36.0 + - - +
188A LEU* 3.1 30.1 + - - +
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Residues in contact with VAL 113 (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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87A VAL* 4.5 6.1 - - + -
91A MET 4.4 2.9 - - - +
92A GLY* 3.3 10.1 - - - -
93A GLY 2.7 34.7 + - - +
95A TYR* 3.4 34.8 - - + +
111A TRP 5.1 0.7 - - - +
112A THR* 1.3 78.2 - - - +
114A ASN* 1.3 64.3 + - - +
115A VAL* 4.1 18.4 - - + -
122A PHE* 3.5 6.9 - - - -
188A LEU* 4.0 5.4 - - + -
190A MET* 3.8 23.6 - - + -
196A LEU* 3.7 26.2 - - + -
198A LEU* 5.4 2.0 - - + -
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Residues in contact with ASN 114 (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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112A THR* 3.3 20.2 + - - -
113A VAL* 1.3 80.3 + - - +
115A VAL* 1.3 60.9 + - - +
116A GLU 4.3 0.2 - - - -
120A GLU 5.2 3.4 - - - +
121A LEU* 3.8 10.8 - - + +
122A PHE* 2.9 40.0 + - - +
123A ARG* 3.3 20.9 + - - +
187A ASP 4.7 0.4 - - - -
188A LEU 2.6 28.3 + - - +
189A THR* 4.0 13.7 - - + +
190A MET* 3.0 31.9 + - - +
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Residues in contact with VAL 115 (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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87A VAL* 4.3 9.0 - - + -
88A SER 4.7 0.4 - - - -
89A GLN* 3.8 43.7 - - + +
92A GLY* 4.1 13.2 - - - +
113A VAL* 4.1 17.7 - - + -
114A ASN* 1.3 77.5 - - - +
116A GLU* 1.3 71.9 + - - +
117A GLY 3.8 0.2 - - - -
118A SER* 3.0 29.4 + - - +
120A GLU 5.3 0.4 + - - -
122A PHE* 6.1 0.2 - - - -
189A THR* 5.9 0.2 - - - -
190A MET* 3.4 4.3 - - + +
191A ALA 4.2 1.1 - - - +
192A PRO* 3.8 33.2 - - + -
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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