Contacts of the strand formed by residues 102 - 108 (chain A) in PDB entry 6BM0
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 LYS 102 (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 3.5 1.6 - - - +
97A SER* 3.4 4.9 - - - -
98A PHE* 2.8 55.0 + - + +
99A LYS 3.1 18.8 + - - +
100A ASP* 4.1 5.6 + - - +
101A ALA* 1.3 78.9 - - - +
103A LEU* 1.3 60.5 + - - +
104A SER* 6.2 0.2 - - - -
120A LEU* 6.6 0.4 - - + -
121A HIS 3.8 5.8 - - - +
122A TYR* 4.2 31.9 - - + -
124A GLU* 3.8 28.3 + - - -
152A MET* 4.0 4.7 - - - +
1376A LEU* 4.5 16.2 - - + -
1380A ALA* 6.3 2.5 - - - -
1387A ASP* 4.7 9.7 + - - -
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Residues in contact with LEU 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* 4.6 13.7 - - + -
96A LEU 3.7 4.5 - - - +
101A ALA 4.3 0.4 - - - -
102A LYS* 1.3 74.9 - - - +
104A SER* 1.3 76.1 + - - +
105A VAL* 3.7 28.0 - - + +
120A LEU* 3.7 4.3 - - - +
121A HIS* 3.2 52.0 + - + +
123A PHE* 5.0 5.1 - - + -
141A VAL* 4.1 16.2 - - + -
151A ALA 5.8 0.9 - - - +
152A MET* 3.6 35.6 - - + +
160A VAL* 6.1 0.9 - - + -
162A LEU* 3.8 28.3 - - + -
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Residues in contact with SER 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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94A LEU 3.5 0.7 - - - +
96A LEU* 3.2 39.0 + - - +
98A PHE* 4.4 8.5 - - - -
102A LYS* 6.2 0.2 - - - -
103A LEU* 1.3 78.8 - - - +
105A VAL* 1.3 62.0 + - - +
106A VAL* 3.5 10.2 + - - +
117A THR* 5.2 0.7 - - - -
119A SER 3.4 6.3 + - - -
120A LEU* 3.7 12.3 - - - +
1374A ALA* 3.3 39.9 + - - +
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Residues in contact with VAL 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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86A LEU* 5.3 0.9 - - + -
93A ALA* 4.0 17.5 - - + -
94A LEU 3.3 4.7 - - - +
95A LEU* 3.9 21.3 - - + -
103A LEU* 3.7 21.9 - - + +
104A SER* 1.3 69.8 - - - +
106A VAL* 1.3 56.4 + - - +
117A THR* 4.0 0.2 - - - -
118A LEU* 2.7 42.8 + - + -
119A SER* 3.1 23.8 + - - +
121A HIS* 5.5 0.4 - - + -
162A LEU* 5.1 4.7 - - + -
164A PHE* 6.2 1.6 - - + -
185A PHE* 3.7 33.4 - - + -
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Residues in contact with VAL 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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22A PHE* 6.2 0.4 - - + -
38A LEU* 5.8 0.2 - - + -
93A ALA* 3.5 3.7 - - - +
94A LEU* 2.9 45.1 + - + +
96A LEU* 3.7 24.9 - - + -
104A SER* 3.5 19.5 + - - +
105A VAL* 1.3 78.8 - - - +
107A GLU* 1.3 61.3 + - - +
115A LEU* 3.8 20.2 - - + -
116A LYS 3.1 18.4 - - - +
117A THR* 3.8 18.4 - - + -
118A LEU* 4.1 1.1 - - - +
1374A ALA* 4.0 9.6 - - + -
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Residues in contact with GLU 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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22A PHE* 5.1 3.1 - - - -
86A LEU* 4.7 5.4 - - - +
89A ALA* 4.1 20.5 - - - +
91A ARG* 3.7 29.8 + - + +
92A ASP 4.8 3.1 - - - +
93A ALA* 3.7 24.5 + - + +
94A LEU* 6.2 0.2 - - - -
106A VAL* 1.3 79.9 - - - +
108A TYR* 1.3 62.7 + - - +
115A LEU* 3.2 7.2 - - - +
116A LYS* 2.6 48.0 + - - +
118A LEU* 3.6 35.4 - - + +
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Residues in contact with TYR 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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22A PHE* 3.3 61.2 + + + +
23A PHE* 3.5 34.1 - + + -
72A PHE* 4.9 3.8 - + - -
91A ARG* 3.0 36.9 + - - +
92A ASP 5.4 1.8 + - - -
107A GLU* 1.3 78.8 - - - +
109A ASP* 1.3 82.3 + - - +
110A PRO* 4.0 12.8 - - + +
113A HIS* 3.1 47.7 + + - -
114A ASP 4.7 0.9 - - - -
115A LEU* 4.2 7.0 - - - +
116A LYS* 5.0 1.8 - - - -
877A PHE* 5.0 3.1 - - - +
878A PRO 5.6 1.2 + - - -
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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