Contacts of the helix formed by residues 89 - 99 (chain A) in PDB entry 3COG
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 SER 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A PHE* 3.1 2.7 - - - +
88A ALA* 1.3 80.3 - - - +
90A GLY* 1.3 58.3 + - - +
91A LEU 3.5 2.6 + - - -
92A ALA* 3.0 17.0 + - - +
93A ALA 2.9 23.6 + - - -
221A VAL* 3.6 14.1 - - - -
222A MET* 3.5 5.8 - - - +
223A GLY* 3.2 18.5 - - - +
500A PLP 3.5 12.1 + - - -
62B ARG* 4.0 4.0 - - - -
244B GLY* 2.6 28.0 + - - -
246B VAL* 4.8 0.2 - - - -
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Residues in contact with GLY 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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89A SER* 1.3 70.5 - - - +
91A LEU* 1.3 56.2 + - - +
93A ALA 3.2 1.4 + - - -
94A THR* 2.9 31.4 + - - -
207A MET* 3.3 21.0 - - - +
209A SER* 4.0 6.1 - - - -
222A MET 3.5 4.0 + - - -
223A GLY* 3.9 8.3 - - - -
500A PLP 3.0 29.3 + - - -
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Residues in contact with LEU 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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89A SER* 3.3 3.8 - - - +
90A GLY* 1.3 74.8 - - - +
92A ALA* 1.3 58.0 + - - +
94A THR* 3.1 8.8 + - - +
95A VAL* 2.8 32.1 + - - +
114A TYR* 4.5 5.2 - - + -
116A GLY* 3.3 32.3 - - - +
117A THR* 3.9 9.0 - - - +
119A ARG* 3.6 13.2 - - - +
120A TYR* 4.8 4.9 - - + -
500A PLP 3.0 20.1 + - + +
62B ARG* 3.2 31.2 - - - +
241B ASN 3.3 17.9 - - - +
242B SER 3.5 14.1 - - - +
243B LEU 3.5 13.2 - - - +
244B GLY* 4.3 0.4 - - - -
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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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87A PHE* 4.4 1.3 - - - -
88A ALA 4.4 0.2 - - - +
89A SER* 3.0 28.9 + - - +
91A LEU* 1.3 72.3 - - - +
93A ALA* 1.3 57.2 + - - +
95A VAL* 3.8 4.1 - - - +
96A THR* 2.7 38.7 + - - -
245A ALA* 3.6 31.6 - - + +
243B LEU 3.2 11.5 + - - +
244B GLY 3.7 10.8 - - - +
245B ALA* 4.3 1.1 - - - +
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Residues in contact with ALA 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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87A PHE* 3.8 19.9 - - + +
89A SER 2.9 13.7 + - - +
90A GLY 3.2 10.5 + - - +
92A ALA* 1.3 75.0 - - - +
94A THR* 1.3 57.5 + - - +
96A THR* 3.4 2.6 + - - -
97A ILE* 3.0 36.3 + - - +
207A MET* 4.2 10.1 - - + -
223A GLY* 4.2 9.4 - - - -
224A LEU 4.4 1.3 - - - +
225A VAL* 3.7 23.4 - - + +
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Residues in contact with THR 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 GLY 2.9 15.1 + - - -
91A LEU* 3.3 13.6 - - + +
93A ALA* 1.3 73.0 - - - +
95A VAL* 1.3 59.6 + - - +
97A ILE* 3.4 2.4 + - - +
98A THR* 2.7 33.0 + - - -
117A THR* 4.6 13.7 + - + +
120A TYR* 3.9 23.1 - - + -
121A PHE* 4.0 13.2 - - + -
155A TRP* 3.3 43.5 - - + -
207A MET* 3.5 4.9 - - - +
500A PLP 5.6 0.3 - - - -
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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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91A LEU* 2.8 24.1 + - + +
92A ALA* 3.8 6.7 - - - +
94A THR* 1.3 72.7 - - - +
96A THR* 1.3 62.5 + - - +
98A THR* 3.2 3.5 + - - -
99A HIS* 2.7 50.9 + - + +
120A TYR* 3.7 26.7 - - + +
243A LEU* 5.1 3.8 - - + -
95B VAL* 5.5 4.0 - - + -
99B HIS* 4.9 2.5 - - + +
242B SER 4.5 0.7 - - - +
243B LEU* 3.7 46.9 - - + +
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Residues in contact with THR 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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87A PHE* 3.6 35.7 - - + -
92A ALA 2.7 23.5 + - - -
93A ALA 3.8 3.6 - - - -
95A VAL* 1.3 75.4 - - - +
97A ILE* 1.3 62.9 + - - +
99A HIS* 2.9 18.2 + - - +
236A LEU* 4.5 7.2 - - + +
239A LEU* 3.3 47.2 + - + +
240A GLN 4.0 0.7 - - - +
243A LEU* 4.1 15.1 - - + +
245A ALA* 4.5 8.0 - - - +
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Residues in contact with ILE 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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87A PHE* 6.1 0.2 - - + -
93A ALA 3.0 21.8 + - - +
94A THR 3.8 3.8 - - - +
96A THR* 1.3 75.2 - - - +
98A THR* 1.3 63.1 + - - +
100A LEU* 3.1 31.6 + - + +
101A LEU* 4.5 1.0 + - - +
153A LEU* 4.2 14.8 - - + +
155A TRP* 3.6 29.2 - - + -
185A VAL* 4.0 20.4 - - + -
205A ILE* 4.2 19.7 - - + -
207A MET* 4.2 8.5 - - + -
225A VAL* 4.0 21.3 - - + -
236A LEU* 4.1 22.2 - - + -
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Residues in contact with THR 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 THR 2.7 21.9 + - - -
95A VAL 3.5 0.9 - - - -
96A THR 3.2 0.2 - - - -
97A ILE* 1.3 75.3 - - - +
99A HIS* 1.3 58.3 + - - +
100A LEU 3.1 0.7 - - - -
101A LEU* 3.1 24.8 + - - +
107A ILE* 3.7 19.7 - - + -
120A TYR* 3.3 37.8 - - + +
121A PHE* 3.5 12.0 - - - -
125A ALA* 4.3 1.6 - - + -
130A LEU* 3.7 24.0 - - + -
153A LEU* 4.6 9.2 - - - +
155A TRP* 5.5 0.3 - - - -
128B PHE* 3.9 5.0 - - - -
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Residues in contact with HIS 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 48.3 + - + +
96A THR 2.9 11.3 + - - +
98A THR* 1.3 74.2 - - + +
100A LEU* 1.3 53.8 + - - +
101A LEU 3.1 5.8 - - - +
120A TYR* 4.2 6.0 + - - -
239A LEU* 3.4 21.0 - - + +
243A LEU* 3.7 18.9 - - + +
603A GOL 2.7 33.1 + - - -
95B VAL* 4.8 1.5 - - + +
99B HIS* 3.6 30.1 + + - -
120B TYR* 5.0 3.0 + + - -
124B VAL* 3.6 24.5 - - + -
125B ALA* 6.4 0.2 - - - -
128B PHE* 3.7 22.0 - + + -
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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