Contacts of the helix formed by residues 87 - 99 (chain A) in PDB entry 1P4K
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 ASN 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ARG* 3.3 46.5 - - - +
43A GLU* 3.1 20.7 - - - +
44A ASP* 2.9 26.4 + - - +
85A ILE* 3.3 4.3 - - - +
86A LYS* 1.3 93.6 - - - +
88A PRO* 1.3 63.7 - - - +
89A ILE 3.2 2.7 - - - -
90A SER* 3.1 14.2 + - - +
91A VAL* 3.4 15.4 + - - +
118A PHE* 4.2 7.4 - - + -
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Residues in contact with PRO 88 (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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43A GLU* 3.2 16.8 - - + +
52A GLY* 5.4 0.2 - - - -
65A LEU* 3.6 35.0 - - + -
66A ASP 4.7 1.3 - - - +
67A ALA* 3.9 8.1 - - + -
79A VAL* 3.6 13.9 - - + +
82A MET* 3.6 28.7 - - + -
85A ILE 3.7 1.7 - - - +
86A LYS 3.2 14.1 - - - +
87A ASN* 1.3 85.5 - - - +
89A ILE* 1.3 55.0 + - - +
91A VAL* 3.0 1.3 + - + +
92A ALA* 2.8 30.1 + - - +
169A THR* 3.5 11.9 - - - +
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Residues in contact with ILE 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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36A GLU* 4.2 8.1 - - + +
39A VAL* 3.7 22.4 - - + -
40A ARG* 3.6 20.4 - - + -
43A GLU* 3.0 31.3 + - - +
67A ALA* 3.8 5.1 - - + +
68A CYS* 3.1 35.7 - - - +
69A ILE* 3.8 14.5 - - + +
88A PRO* 1.3 76.6 - - - +
90A SER* 1.3 63.3 + - - +
92A ALA* 3.4 3.2 + - + +
93A ARG* 3.0 24.9 + - - +
167A ALA* 3.5 19.5 - - + -
168A CYS 3.9 10.8 - - - +
169A THR* 4.6 0.9 - - - -
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Residues in contact with SER 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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36A GLU* 2.7 27.4 + - - +
40A ARG* 2.8 32.9 + - - -
87A ASN* 3.1 9.7 + - - +
89A ILE* 1.3 79.1 - - - +
91A VAL* 1.3 65.1 + - - +
93A ARG* 3.3 4.3 + - - +
94A ALA* 3.0 17.7 + - - +
118A PHE* 3.6 25.1 - - - -
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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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79A VAL* 3.8 17.3 - - + -
82A MET* 3.6 27.4 - - + -
85A ILE* 3.7 16.6 - - + -
87A ASN 3.6 11.2 - - - +
88A PRO 3.0 5.1 + - - +
90A SER* 1.3 76.2 - - - +
92A ALA* 1.3 59.3 + - - +
94A ALA* 3.0 5.2 + - - +
95A VAL* 2.8 25.8 + - - +
109A ALA 4.3 1.3 - - - +
112A PHE* 4.0 18.4 - - + -
113A ALA* 3.8 25.1 - - + -
118A PHE* 3.9 15.0 - - + -
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Residues in contact with ALA 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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67A ALA 3.9 16.2 - - - +
68A CYS* 4.2 3.8 - - - -
69A ILE* 4.0 7.0 - - + +
77A GLY* 3.3 32.0 - - - +
78A SER* 3.9 6.1 - - - +
79A VAL* 4.1 9.1 - - - +
88A PRO 2.8 13.2 + - - +
89A ILE* 3.4 12.6 - - - +
90A SER 3.2 0.2 - - - -
91A VAL* 1.3 77.6 - - - +
93A ARG* 1.3 60.8 - - - +
95A VAL* 3.1 2.9 + - - +
96A MET 3.0 18.7 + - - -
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Residues in contact with ARG 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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30A LYS* 4.3 11.1 - - - +
32A LEU* 3.6 26.9 + - - +
33A ASP* 2.7 35.9 + - - +
36A GLU* 2.8 38.7 + - - +
69A ILE* 3.9 23.3 - - + +
89A ILE 3.0 14.0 + - - +
90A SER* 3.6 11.9 - - - +
91A VAL 3.2 0.2 - - - -
92A ALA* 1.3 76.5 - - - +
94A ALA* 1.3 58.1 + - - +
96A MET* 3.3 8.7 + - + +
97A GLU* 2.8 62.3 + - + +
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Residues in contact with ALA 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 SER 3.0 12.7 + - - +
91A VAL* 3.0 12.0 + - - +
93A ARG* 1.3 76.2 - - - +
95A VAL* 1.3 60.1 + - - +
97A GLU* 4.8 2.7 - - - -
98A LYS* 2.8 43.7 + - + +
112A PHE* 3.5 20.5 - - + -
116A GLN* 4.4 14.8 - - + +
118A PHE* 4.4 8.1 - - + -
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Residues in contact with VAL 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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78A SER 4.0 5.4 - - - +
79A VAL* 3.9 22.2 - - + -
91A VAL 2.8 16.9 + - - +
92A ALA* 3.1 8.5 + - - +
94A ALA* 1.3 76.9 - - - +
96A MET* 1.3 65.0 + - - +
99A THR* 2.7 32.9 + - - +
101A HIS 3.4 18.8 - - - +
102A VAL* 3.7 23.8 - - - +
103A MET 3.9 3.6 - - - +
104A LEU* 3.9 18.4 - - + -
112A PHE* 3.7 23.3 - - + -
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Residues in contact with MET 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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32A LEU* 4.1 33.2 - - + -
69A ILE* 4.2 10.8 - - + +
71A ASP* 4.5 7.2 - - + +
75A ASN* 3.4 42.0 - - + +
76A ILE* 3.3 35.9 - - - +
77A GLY* 3.7 1.6 - - - -
92A ALA 3.0 9.9 + - - +
93A ARG* 3.4 14.1 - - + +
95A VAL* 1.3 81.5 - - - +
97A GLU* 1.3 77.5 + - + +
99A THR 4.0 8.3 - - - +
101A HIS 4.7 1.6 - - - +
546C ARG* 5.9 1.4 + - - -
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Residues in contact with GLU 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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32A LEU* 4.2 7.1 - - - +
93A ARG* 2.8 66.5 + - - +
94A ALA* 5.2 0.9 - - - -
96A MET* 1.3 86.3 - - + +
98A LYS* 1.3 86.2 + - + +
99A THR 3.7 0.8 - - - +
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Residues in contact with LYS 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 ALA* 2.8 28.3 + - + +
97A GLU* 1.3 99.8 + - + +
99A THR* 1.3 62.0 + - - +
100A PRO* 4.9 0.2 - - - +
112A PHE* 4.2 12.3 - - + -
116A GLN* 3.7 25.6 + - - +
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Residues in contact with THR 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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95A VAL* 2.7 30.4 + - + +
96A MET 4.0 7.4 - - - +
97A GLU 3.7 1.1 - - - -
98A LYS* 1.3 83.1 - - - +
100A PRO* 1.3 71.2 - - - +
101A HIS* 3.0 23.2 + - - +
104A LEU* 5.1 1.8 - - + -
112A PHE* 3.5 35.0 - - + -
477C MET* 3.8 21.8 - - + -
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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