Contacts of the helix formed by residues 88 - 100 (chain A) in PDB entry 2LKT
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 PRO 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ARG* 1.4 82.7 - - + +
89A VAL* 1.3 64.0 + - - +
90A GLU 3.3 2.5 - - - -
91A VAL* 2.9 38.7 + - + -
92A ILE* 3.1 19.5 + - + +
123A GLY* 5.3 5.8 - - - -
124A LYS* 3.7 29.2 - - + +
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Residues in contact with VAL 89 (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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10A PRO* 3.3 31.4 - - + +
11A GLY* 4.2 2.7 - - - -
12A ASP* 5.3 1.1 - - - +
86A PRO 5.5 0.4 - - - +
87A ARG* 3.1 32.6 + - - +
88A PRO* 1.3 69.6 - - - +
90A GLU* 1.3 65.4 + - + +
92A ILE* 3.3 11.5 + - - +
93A ILE* 3.1 29.8 + - + +
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Residues in contact with GLU 90 (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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88A PRO 3.1 1.0 + - - -
89A VAL* 1.3 80.2 - - + +
91A VAL* 1.3 58.0 + - + +
93A ILE* 3.5 9.4 + - + +
94A SER* 2.7 37.5 + - - +
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Residues in contact with VAL 91 (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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88A PRO* 2.9 32.1 + - + +
90A GLU* 1.3 77.0 - - + +
92A ILE* 1.3 58.6 + - + +
94A SER* 3.7 8.1 - - - +
95A SER* 2.8 43.5 + - - +
123A GLY* 6.2 2.9 - - - -
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Residues in contact with ILE 92 (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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11A GLY 3.5 21.3 - - - +
26A LEU* 4.0 17.0 - - + -
85A GLN* 5.4 0.2 - - - +
87A ARG* 3.5 37.2 - - + +
88A PRO* 3.1 27.3 + - + +
89A VAL* 3.3 6.7 + - - +
91A VAL* 1.3 76.0 - - + +
93A ILE* 1.3 58.9 + - - +
95A SER* 3.2 2.8 + - - -
96A ALA* 2.9 29.2 + - - +
120A LEU 3.5 18.1 - - - +
121A ARG* 3.7 28.5 - - + +
123A GLY* 5.0 5.8 - - - -
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Residues in contact with ILE 93 (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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10A PRO* 4.0 13.2 - - + -
11A GLY* 3.5 36.3 - - - +
26A LEU* 4.6 1.1 - - + -
27A TYR 4.3 4.5 - - - +
28A ILE* 3.5 32.7 - - + +
89A VAL* 3.1 18.0 + - + +
90A GLU* 3.7 10.8 - - + +
92A ILE* 1.3 73.4 - - - +
94A SER* 1.3 62.1 + - - +
96A ALA* 3.5 7.4 + - - +
97A LYS* 3.1 42.1 + - - +
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Residues in contact with SER 94 (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 GLU* 2.7 23.1 + - - +
91A VAL* 3.7 10.6 - - - +
93A ILE* 1.3 77.4 - - - +
95A SER* 1.3 55.2 + - - +
97A LYS* 3.3 15.8 + - - +
98A GLU* 3.0 37.0 + - - +
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Residues in contact with SER 95 (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 VAL* 2.8 31.6 + - - +
92A ILE* 3.2 5.8 + - - -
94A SER* 1.3 72.2 - - - +
96A ALA* 1.3 58.5 + - - +
98A GLU* 3.1 16.4 + - - +
99A MET* 2.8 33.9 + - - +
119A GLN 4.5 7.4 - - - -
120A LEU* 3.6 18.1 + - - -
121A ARG 4.5 6.1 + - - -
122A TYR* 5.9 0.7 - - - +
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Residues in contact with ALA 96 (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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26A LEU* 4.0 10.5 - - + -
28A ILE* 3.6 26.5 - - + -
34A ILE* 3.9 15.7 - - + +
92A ILE 2.9 16.4 + - - +
93A ILE 3.6 0.7 - - - +
95A SER* 1.3 75.1 - - - +
97A LYS* 1.3 56.9 + - - +
99A MET* 3.1 2.4 + - - +
100A VAL 3.0 25.8 + - - -
120A LEU* 3.7 28.4 - - + +
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Residues in contact with LYS 97 (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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28A ILE* 4.2 29.1 + - + +
34A ILE* 5.0 1.8 - - + -
62A ARG* 6.0 1.3 - - - -
93A ILE* 3.1 36.6 + - + +
94A SER* 3.6 11.4 - - - +
96A ALA* 1.3 74.6 - - - +
98A GLU* 1.3 59.0 + - - +
100A VAL* 3.3 24.1 - - + +
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Residues in contact with GLU 98 (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 SER* 3.0 20.7 + - - +
95A SER* 3.1 17.8 + - - +
97A LYS* 1.3 77.9 - - - +
99A MET* 1.3 63.9 + - + +
100A VAL* 3.3 9.0 + - - +
102A GLN* 5.5 2.4 - - - +
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Residues in contact with MET 99 (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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60A VAL* 3.3 28.1 - - + +
95A SER* 2.8 22.9 + - - +
96A ALA* 3.7 7.9 - - - +
98A GLU* 1.3 72.9 - - + +
100A VAL* 1.3 63.8 + - - +
101A GLY 3.2 0.5 + - - -
102A GLN* 3.0 49.1 + - + +
104A MET* 5.6 2.0 - - - -
116A PHE* 4.5 7.9 - - + -
119A GLN* 3.7 59.5 - - + +
120A LEU* 4.3 10.5 - - + -
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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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34A ILE* 3.9 14.8 - - + -
60A VAL* 4.1 8.4 - - - +
61A LYS* 4.5 1.3 - - - -
62A ARG* 3.8 41.1 - - + +
96A ALA 3.0 7.6 + - - +
97A LYS* 3.3 25.1 - - - +
98A GLU 3.7 6.8 - - - +
99A MET* 1.3 73.8 - - - +
101A GLY* 1.3 62.8 + - - +
102A GLN 3.6 0.3 + - - -
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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