Contacts of the helix formed by residues 91 - 98 (chain U) in PDB entry 3EXG
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 ALA 91 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87U THR* 3.8 26.0 - - + -
88U ALA 3.9 0.7 - - - +
89U TYR* 3.2 6.2 + - - +
90U ARG* 1.3 74.1 - - - +
92U HIS* 1.3 62.6 + - + +
93U GLY 3.2 2.9 - - - -
94U PHE* 3.0 6.0 + - - -
95U THR* 2.8 33.3 + - - +
123U SER 5.1 2.5 - - - +
124U MET 5.8 0.2 - - - -
126U MET* 4.8 7.6 - - + -
131U PHE* 4.1 8.5 - - + -
134U GLY* 3.8 20.4 - - - +
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Residues in contact with HIS 92 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45U MET* 4.5 8.1 - - - +
46U GLU* 3.4 32.3 + - - +
62U CYS* 4.6 3.4 - - - -
63U HIS 3.4 24.7 + - - -
64U LEU* 4.2 6.7 - - + +
65U CYS* 5.1 0.2 - - - -
89U TYR 4.8 1.0 + - - -
90U ARG 3.6 1.8 - - - -
91U ALA* 1.3 80.0 - - - +
93U GLY* 1.3 63.5 + - - +
95U THR* 3.3 3.5 + - - -
96U PHE* 3.2 19.8 + - - +
105U ILE* 4.0 13.8 - - + +
109U LEU* 3.9 23.8 - - + +
123U SER* 2.8 41.6 + - - -
126U MET* 3.3 27.8 - - + -
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Residues in contact with GLY 93 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42U VAL* 4.0 18.3 - - - +
45U MET* 5.8 1.3 - - - -
65U CYS* 3.5 27.2 - - - +
72U CYS* 4.1 9.9 - - - -
90U ARG 4.9 0.2 + - - -
91U ALA 3.2 0.6 - - - -
92U HIS* 1.3 78.6 - - - +
94U PHE* 1.3 57.3 + - - +
96U PHE* 3.0 4.9 + - - +
97U THR* 2.8 31.8 + - - +
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Residues in contact with PHE 94 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65U CYS* 6.3 2.2 - - + -
68U GLN* 5.9 0.7 - - - -
71U CYS* 4.6 5.2 - - + -
72U CYS* 3.5 37.5 - - + -
75U LEU* 3.8 12.6 - - + -
76U GLU* 5.9 1.1 - - - -
85U LEU* 3.7 35.4 - - + -
87U THR* 4.4 11.7 - - + -
90U ARG 4.4 15.7 - - - -
91U ALA 3.0 6.6 + - - +
93U GLY* 1.3 75.8 - - - +
95U THR* 1.3 63.2 + - - +
97U THR* 3.1 19.4 + - - -
98U ARG* 3.3 19.4 + - + +
131U PHE* 4.0 18.8 - - + -
164U LEU* 3.3 23.3 - - + -
194U GLU* 3.5 20.2 - - - -
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Residues in contact with THR 95 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91U ALA* 2.8 16.8 + - - +
92U HIS 3.5 8.3 - - - -
93U GLY 3.2 0.2 - - - -
94U PHE* 1.3 78.8 - - - +
96U PHE* 1.3 59.7 + - - +
98U ARG* 3.7 6.0 + - - +
99U GLY 4.1 0.3 + - - -
100U LEU* 3.0 60.0 + - + +
105U ILE* 3.6 12.3 - - + -
126U MET* 3.4 30.6 - - + +
128U ALA* 5.0 0.6 - - + +
131U PHE* 3.4 26.3 - - + -
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Residues in contact with PHE 96 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U MET* 4.1 26.7 - - + -
41U THR* 3.8 29.8 - - + -
42U VAL* 3.8 21.8 - - + -
45U MET* 4.7 5.4 - - + -
92U HIS 3.2 5.6 + - - +
93U GLY 3.0 7.9 + - - +
95U THR* 1.3 75.9 - - - +
97U THR* 1.3 59.9 + - + +
98U ARG 2.7 16.3 + - - -
99U GLY* 3.2 10.9 + - - -
100U LEU 3.2 23.8 - - - +
101U SER* 5.0 1.8 - - - -
102U VAL* 3.9 27.8 - - + -
105U ILE* 3.7 12.1 - - + +
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Residues in contact with THR 97 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U MET* 5.0 11.9 - - - +
42U VAL* 4.5 2.0 - - + -
72U CYS* 3.8 42.8 + - + +
73U VAL* 4.1 13.7 - - + -
76U GLU* 3.1 35.4 + - - +
93U GLY 2.8 19.6 + - - +
94U PHE* 3.1 23.6 + - - -
96U PHE* 1.3 81.5 - - + +
98U ARG* 1.3 56.0 + - - +
99U GLY 3.6 1.0 + - - -
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Residues in contact with ARG 98 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76U GLU* 3.2 36.8 + - - +
79U ILE* 3.8 15.5 - - - +
80U ASN 3.3 24.5 + - - -
81U PRO* 3.6 12.6 + - - +
83U ASP 2.8 24.6 + - - -
84U HIS* 4.3 1.4 - - - +
85U LEU* 4.3 13.5 - - + +
94U PHE* 3.3 17.9 - - + +
95U THR 4.1 4.7 - - - +
96U PHE 2.7 6.9 + - - -
97U THR* 1.3 74.5 - - - +
99U GLY* 1.3 56.9 + - - +
100U LEU 3.7 2.6 + - - -
128U ALA* 4.1 12.2 - - + +
129U LYS* 4.0 13.2 + - - +
130U ASN* 3.1 32.3 + - - +
131U PHE* 4.1 29.6 - - + -
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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