Contacts of the strand formed by residues 99 - 104 (chain A) in PDB entry 3LBF
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 HIS 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A SER 3.7 1.6 + - - +
78A ARG* 3.8 3.7 - - + +
79A VAL 3.0 24.8 + - - +
97A VAL* 3.4 8.1 - - - +
98A GLN* 1.3 102.9 - - - +
100A VAL* 1.3 82.0 + - - +
101A CYS* 3.9 8.2 - - - -
123A HIS 4.9 2.0 + - - -
124A ASN* 3.4 24.3 + - + +
125A VAL 4.3 1.0 + - - -
126A SER* 2.8 36.9 + - - -
139A ARG* 3.6 14.4 + - - -
211A PO4 3.5 21.4 + - - -
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Residues in contact with VAL 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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79A VAL* 3.5 8.7 - - + +
81A GLU* 4.4 3.8 - - + -
90A THR* 4.2 17.5 - - + +
93A LEU* 3.7 37.9 - - + -
94A ALA* 3.8 16.8 - - + +
97A VAL* 3.5 25.8 - - + -
99A HIS* 1.3 78.4 + - - +
101A CYS* 1.3 68.4 + - - +
124A ASN 2.9 9.1 + - - +
125A VAL* 3.2 10.5 - - + +
126A SER 2.7 31.7 + - - +
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Residues in contact with CYS 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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79A VAL 2.8 14.7 + - - +
80A LEU* 3.3 10.9 - - + +
81A GLU 2.7 32.1 + - - -
99A HIS* 3.9 8.7 - - - -
100A VAL* 1.3 79.4 - - - +
102A SER* 1.3 54.5 + - - +
126A SER* 3.2 6.5 - - - -
136A TRP* 3.6 20.4 - - + -
139A ARG* 3.8 47.6 - - - -
142A PHE* 4.3 6.5 - - + -
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Residues in contact with SER 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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81A GLU* 2.6 33.6 + - - -
84A THR* 2.6 31.5 + - - +
90A THR* 4.0 16.8 - - - -
100A VAL* 4.7 0.4 - - - -
101A CYS* 1.3 76.0 - - - +
103A VAL* 1.3 57.6 + - - +
126A SER 2.7 12.7 + - - -
127A THR* 3.3 6.5 - - - -
128A ARG* 2.8 34.0 + - - +
136A TRP* 3.8 1.2 - - - -
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Residues in contact with VAL 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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80A LEU* 3.9 8.1 - - + -
81A GLU 2.9 5.5 + - - -
82A ILE* 3.9 22.9 - - + -
83A GLY 2.7 33.1 + - - -
84A THR* 3.3 5.4 + - - -
102A SER* 1.3 77.7 + - - +
104A GLU* 1.3 58.4 + - - +
128A ARG* 3.3 15.3 - - + +
130A GLY* 3.5 31.4 - - - +
131A ASP 4.2 1.3 - - - +
132A GLY* 3.9 15.0 - - - +
135A GLY 4.3 10.8 - - - +
136A TRP* 3.8 23.3 - - + -
300A SAH 3.6 2.9 - - + -
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Residues in contact with GLU 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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83A GLY 3.5 2.3 - - - -
84A THR* 3.2 25.5 + - - +
85A GLY 2.8 18.7 + - - +
103A VAL* 1.3 71.8 - - - +
105A ARG* 1.3 61.3 + - - +
106A ILE* 3.0 37.0 + - - +
109A LEU* 4.0 7.4 - - + -
110A GLN* 3.8 20.3 - - + +
128A ARG 2.9 6.9 + - - -
129A HIS* 3.2 13.7 + - - -
130A GLY 3.0 19.7 + - - -
300A SAH 2.6 49.2 + - - -
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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