Contacts of the helix formed by residues 88 - 100 (chain A) in PDB entry 3CVU
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 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASP* 3.4 30.9 + - - +
87A GLY* 1.3 74.3 - - - -
89A PRO* 1.3 69.5 - - + +
90A ALA* 4.4 8.1 - - + +
91A GLU* 3.0 25.7 + - + +
92A VAL* 2.8 27.6 + - - +
114A TYR* 5.7 5.4 - - - -
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Residues in contact with PRO 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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11A TRP* 4.1 24.9 - - + -
45A ILE* 4.2 12.7 - - + -
47A ASP* 6.2 0.9 - - + -
87A GLY 4.2 4.5 - - - +
88A LYS* 1.3 84.9 - - + +
90A ALA* 1.3 63.0 + - - +
92A VAL* 4.3 4.9 - - + -
93A PHE* 3.0 50.2 + - + +
94A PRO* 3.9 0.2 - - - +
114A TYR* 5.4 7.2 - - - +
118A ARG* 4.3 18.6 - - + -
122A VAL* 4.5 9.1 - - + +
125A LEU* 5.3 0.3 - - - +
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Residues in contact with ALA 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 LYS* 3.1 7.2 + - + +
89A PRO* 1.3 79.0 - - - +
91A GLU* 1.3 56.2 + - - +
94A PRO* 3.2 23.0 - - - +
125A LEU* 6.2 0.4 - - - -
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Residues in contact with GLU 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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87A GLY* 3.6 9.1 - - - -
88A LYS* 3.0 43.0 + - + +
90A ALA* 1.3 79.8 - - - +
92A VAL* 1.3 74.3 + - + +
94A PRO* 3.5 10.1 - - - +
95A ARG* 3.6 13.5 + - - +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 4.0 22.9 - - + -
85A VAL* 3.8 24.7 - - + -
86A ARG 4.0 8.1 - - - +
87A GLY* 3.8 26.0 - - - -
88A LYS 2.8 25.5 + - - +
89A PRO* 4.2 3.4 - - + +
91A GLU* 1.3 76.0 - - + +
93A PHE* 1.3 59.4 + - - +
95A ARG* 3.2 13.7 + - - +
96A ILE* 2.9 43.7 + - + +
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.9 0.7 - - + -
11A TRP* 3.6 51.1 - + - -
43A ILE* 4.4 4.0 - - + -
45A ILE* 3.7 20.4 - - + -
89A PRO* 3.0 24.3 + - + +
92A VAL* 1.3 73.6 - - - +
94A PRO* 1.3 67.7 - - + +
96A ILE* 3.9 21.5 - - + -
97A PHE* 2.8 61.1 + + + -
105A LEU* 3.9 24.9 - - + -
122A VAL* 3.9 16.6 - - + -
125A LEU* 3.6 16.4 - - + -
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Residues in contact with PRO 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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89A PRO 3.9 0.4 - - - +
90A ALA 3.2 26.7 - - - +
91A GLU* 3.5 8.7 - - - +
93A PHE* 1.3 91.9 - - + +
95A ARG* 1.3 62.4 + - - +
97A PHE* 4.1 3.7 - - + +
98A LYS* 3.4 29.4 + - + +
125A LEU* 3.4 35.2 - - + -
129A GLU* 4.9 1.3 - - - +
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Residues in contact with ARG 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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85A VAL* 3.8 17.2 - - - +
86A ARG 5.7 0.4 + - - -
91A GLU 3.6 10.3 + - - +
92A VAL* 3.2 14.1 + - - +
93A PHE 3.2 0.4 - - - -
94A PRO* 1.3 79.3 - - - +
96A ILE* 1.3 78.1 + - - +
98A LYS* 3.3 7.9 + - - +
99A SER* 2.7 35.6 + - - -
190A ASP* 3.3 21.6 + - - -
191A GLU* 3.3 24.5 + - - +
192A VAL* 3.6 19.7 - - - +
200A TYR* 3.0 20.1 + - - -
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Residues in contact with ILE 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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9A VAL* 5.1 3.8 - - + -
43A ILE* 3.8 22.0 - - + -
85A VAL* 5.0 1.6 - - + -
92A VAL* 2.9 30.3 + - + +
93A PHE* 3.8 24.2 - - + +
95A ARG* 1.3 107.0 - - - +
97A PHE* 1.3 71.9 + - + +
99A SER* 3.5 6.1 - - - -
100A TRP* 2.9 75.1 + - + +
102A VAL* 3.4 1.8 - - + +
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Residues in contact with PHE 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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9A VAL* 6.0 0.4 - - + -
93A PHE* 2.8 56.3 + + + +
94A PRO* 4.1 4.0 - - + +
96A ILE* 1.3 74.1 - - + +
98A LYS* 1.3 61.2 + - - +
101A ARG* 3.3 2.9 + - - -
102A VAL* 3.1 48.8 + - + +
105A LEU* 4.1 18.8 - - + -
122A VAL* 4.7 2.9 - - + -
125A LEU* 3.6 31.0 - - + -
126A ALA* 3.8 28.0 - - + -
129A GLU* 4.1 24.8 - - + +
131A VAL* 3.9 23.1 - - + +
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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 PRO* 3.4 16.8 + - + +
95A ARG* 3.3 8.7 + - - +
96A ILE 3.2 0.4 - - - -
97A PHE* 1.3 77.9 - - - +
99A SER* 1.3 65.9 + - - +
101A ARG* 3.2 19.9 + - - +
129A GLU* 3.3 23.8 - - - +
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Residues in contact with SER 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 ARG* 2.7 33.3 + - - -
96A ILE* 3.5 4.9 - - - -
98A LYS* 1.3 74.6 - - - +
100A TRP* 1.3 71.4 + - - +
101A ARG* 3.6 3.8 + - - +
190A ASP* 4.5 1.9 - - - +
191A GLU* 3.0 38.1 + - - -
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Residues in contact with TRP 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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5A ARG 4.8 1.6 - - - +
6A SER* 4.3 0.9 - - - -
7A THR* 2.7 32.6 + - - +
9A VAL* 3.8 20.9 - - + -
41A ARG* 3.8 53.6 - - + +
43A ILE* 3.7 29.8 - - + -
83A PHE* 5.2 0.9 - - + -
85A VAL* 4.2 8.1 - - + -
96A ILE* 2.9 60.6 + - + +
99A SER* 1.3 86.0 + - - +
101A ARG* 1.3 68.2 + - - +
102A VAL* 3.8 6.1 - - + -
190A ASP* 3.0 25.9 + - + -
200A TYR* 4.0 15.5 - + - -
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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