Contacts of the strand formed by residues 99 - 108 (chain A) in PDB entry 2L8K
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 LEU 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A VAL* 5.0 1.8 - - + +
78A THR* 4.8 7.6 - - + +
79A ALA* 4.4 18.6 - - + +
94A HIS* 3.0 5.7 - - - -
95A PHE* 2.8 28.1 + - + +
96A LYS* 2.7 42.7 + - + +
98A ASP* 1.3 76.9 - - - +
100A VAL* 1.3 59.8 + - - +
119A VAL* 3.8 31.4 - - + +
120A VAL* 3.6 5.8 - - - -
121A LYS* 3.5 45.1 - - + +
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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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92A MET* 3.2 51.8 - - + -
93A ALA 3.7 2.5 - - - -
94A HIS* 3.6 29.8 - - + +
98A ASP 3.8 0.8 + - - -
99A LEU* 1.3 73.0 - - - +
101A LEU* 1.3 60.2 + - - +
102A VAL* 3.8 7.9 - - + -
118A ASP 3.4 0.2 - - - +
119A VAL* 3.8 0.6 - - - -
120A VAL* 2.6 49.2 + - + +
122A GLU* 4.4 22.7 - - + +
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Residues in contact with LEU 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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32A LEU* 4.8 12.3 - - + -
83A VAL* 3.0 40.4 - - + -
89A LEU* 4.4 13.9 - - + +
91A ARG 4.3 1.0 - - - +
92A MET* 3.1 5.4 - - - +
93A ALA* 2.6 49.7 + - + +
94A HIS 3.9 5.6 - - - +
95A PHE* 3.5 39.7 - - + -
100A VAL* 1.3 71.0 - - - +
102A VAL* 1.3 62.0 + - - +
103A PRO* 4.2 0.3 - - - +
117A CYS* 3.7 15.9 - - + +
118A ASP 3.5 3.4 - - - -
119A VAL* 4.3 17.5 - - + -
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Residues in contact with VAL 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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92A MET* 3.7 25.8 - - + -
100A VAL* 3.8 1.8 - - + -
101A LEU* 1.3 74.3 - - - +
103A PRO* 1.3 88.0 - - + +
104A LEU* 4.0 0.5 - - - +
117A CYS* 2.8 25.3 - - - +
118A ASP* 3.0 18.8 + - + +
120A VAL* 3.4 28.0 - - + -
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Residues in contact with PRO 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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89A LEU 3.6 17.3 - - - +
90A ASP* 3.3 23.1 - - - +
91A ARG* 3.8 7.0 - - - +
92A MET* 3.7 20.0 - - + +
101A LEU 4.2 0.2 - - - +
102A VAL* 1.3 98.2 - - + +
104A LEU* 1.3 60.6 + - - +
106A THR* 5.8 0.7 - - - +
115A THR* 5.0 1.1 - - + -
116A ILE 4.1 0.2 - - - +
117A CYS* 3.5 12.9 - - - -
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Residues in contact with LEU 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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82A ARG* 3.5 32.5 - - + +
102A VAL 3.2 0.4 + - - +
103A PRO* 1.3 75.2 - - - +
105A THR* 1.3 73.5 + - - +
115A THR* 4.9 0.8 - - - +
116A ILE* 2.6 43.7 + - + +
117A CYS* 3.8 5.4 - - - -
118A ASP* 3.6 31.2 - - + +
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Residues in contact with THR 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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16A PHE* 3.4 33.2 - - + -
104A LEU* 1.3 97.1 + - - +
106A THR* 1.3 64.8 + - - +
107A LYS* 4.1 13.9 - - + +
114A CYS 3.4 2.8 - - - +
115A THR* 3.1 2.0 - - - +
116A ILE* 2.5 42.5 + - - +
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Residues in contact with THR 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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89A LEU 4.3 2.8 + - - -
90A ASP* 4.3 12.1 + - - +
103A PRO* 5.8 0.9 - - - +
105A THR* 1.3 75.1 - - - +
107A LYS* 1.3 71.0 + - - +
108A VAL* 5.3 2.5 - - + -
113A ARG* 4.2 24.5 - - - +
114A CYS 3.3 6.7 - - - +
115A THR* 2.8 35.1 + - - +
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Residues in contact with LYS 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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12A ASP* 5.2 3.8 + - - -
13A ASP* 3.9 23.3 - - - +
16A PHE* 3.3 60.2 - - + +
105A THR* 4.1 10.8 - - + +
106A THR* 1.3 79.6 - - - +
108A VAL* 1.3 62.0 + - - +
109A VAL* 3.9 8.6 + - + +
112A SER 3.6 0.2 - - - +
114A CYS* 2.6 47.9 + - - +
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Residues in contact with VAL 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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106A THR* 5.3 2.5 - - + -
107A LYS* 1.3 75.6 - - - +
109A VAL* 1.3 62.3 + - - +
110A GLY 4.3 0.5 + - - -
111A GLY* 3.9 11.9 - - - +
112A SER 3.2 30.7 - - - +
113A ARG* 3.8 28.7 - - + +
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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