Contacts of the helix formed by residues 85 - 95 (chain Y) in PDB entry 2W4V
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 85 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84Y ASP* 1.6 57.1 - - - +
86Y GLU* 1.3 64.9 + - - +
87Y GLU* 3.0 5.8 - - - +
88Y THR* 1.8 71.6 + - - +
89Y ILE* 2.4 40.3 - - - +
149Y LYS* 3.6 5.8 - - - +
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Residues in contact with GLU 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85Y SER* 1.3 73.2 - - - +
87Y GLU* 1.3 74.5 + - + +
89Y ILE* 2.4 35.3 - - + +
90Y ARG* 3.1 17.8 + - - +
145Y THR* 3.6 6.5 - - + +
146Y ALA* 6.0 1.6 - - - -
149Y LYS* 2.3 46.7 + - + +
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Residues in contact with GLU 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85Y SER* 3.0 5.8 - - - +
86Y GLU* 1.3 99.5 - - + +
88Y THR* 1.3 61.2 + - + +
89Y ILE 3.2 0.2 - - - -
90Y ARG* 3.2 35.7 + - - +
91Y ASN* 2.3 42.7 + - - +
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Residues in contact with THR 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810C VAL* 5.2 3.4 - - - +
84Y ASP* 2.3 37.3 + - + -
85Y SER* 1.8 62.0 + - - +
87Y GLU* 1.3 70.4 - - + +
89Y ILE* 1.3 58.0 + - - -
91Y ASN* 3.7 8.3 + - - +
92Y ALA* 3.3 20.4 + - - +
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Residues in contact with ILE 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810C VAL* 5.3 3.4 - - + -
814C ASN* 4.9 15.0 - - + +
84Y ASP* 2.4 39.3 - - - +
85Y SER 2.4 27.3 + - - +
86Y GLU* 2.4 53.8 - - + +
88Y THR* 1.3 74.0 - - - +
90Y ARG* 1.3 66.4 + - - +
91Y ASN 2.9 6.3 + - - -
92Y ALA* 3.1 15.7 + - - +
93Y PHE 3.2 3.8 + - - -
141Y TYR* 2.8 26.7 + - - +
145Y THR* 2.7 31.2 - - + -
148Y ILE* 5.4 10.1 - - + -
149Y LYS* 4.3 4.0 - - + -
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Residues in contact with ARG 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Y GLU 3.1 15.5 + - - +
87Y GLU* 3.2 39.3 + - - +
89Y ILE* 1.3 82.2 - - - +
91Y ASN* 1.3 81.2 + - - +
93Y PHE* 3.6 3.5 - - + +
94Y ALA* 3.2 24.9 + - - +
102Y LYS* 3.2 30.5 - - + +
141Y TYR* 3.2 20.5 - - + -
142Y VAL* 4.6 27.6 - - + -
145Y THR* 4.4 5.4 - - + +
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Residues in contact with ASN 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Y GLU* 2.3 37.0 + - - +
88Y THR* 3.8 8.2 - - - +
89Y ILE 2.9 0.8 - - - -
90Y ARG* 1.3 98.2 + - - +
92Y ALA* 1.3 56.0 + - - +
93Y PHE 2.7 14.4 + - - -
94Y ALA* 3.0 8.4 + - - +
95Y MET* 2.9 23.2 + - - +
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Residues in contact with ALA 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800C LYS* 4.3 1.0 + - - -
806C ILE* 5.3 2.2 - - + -
807C GLY* 3.0 25.2 - - - +
808C LEU* 5.5 2.1 - - - +
810C VAL* 2.7 45.3 - - + -
811C ILE* 4.0 4.0 - - + +
88Y THR 3.3 9.7 + - - +
89Y ILE 3.1 8.9 + - - +
91Y ASN* 1.3 78.1 - - - +
93Y PHE* 1.3 57.8 + - - +
95Y MET* 3.5 18.8 - - - +
96Y PHE* 5.4 1.2 - - - +
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Residues in contact with PHE 93 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811C ILE* 5.2 2.7 - - + -
89Y ILE 3.2 1.6 + - - -
90Y ARG* 3.6 3.6 - - + +
91Y ASN 2.7 1.4 - - - -
92Y ALA* 1.3 77.8 - - - +
94Y ALA* 1.3 57.5 + - + +
95Y MET 2.7 15.3 + - - -
96Y PHE* 2.8 22.0 + - - +
97Y ASP* 3.6 6.5 + - + -
102Y LYS* 4.9 3.4 - - - -
103Y LYS 4.2 15.5 - - - -
104Y LEU* 2.7 60.1 - - + -
109Y ILE* 4.7 3.8 - - + -
139Y PHE* 3.9 5.2 - + - -
141Y TYR* 2.7 81.0 - + + -
142Y VAL* 5.2 2.5 - - + -
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Residues in contact with ALA 94 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90Y ARG* 3.2 14.1 + - - +
91Y ASN* 3.0 10.8 + - - +
93Y PHE* 1.3 80.7 - - + +
95Y MET* 1.3 55.2 + - - +
96Y PHE 3.0 2.9 - - - -
97Y ASP* 3.1 36.1 + - + +
98Y GLU* 4.4 0.5 + - - -
100Y GLU* 6.4 1.1 - - - -
102Y LYS* 5.3 13.7 - - + +
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Residues in contact with MET 95 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800C LYS* 2.2 95.7 - - + +
803C ASP* 2.5 42.0 - - - +
804C GLN* 3.1 7.0 - - + +
806C ILE* 4.5 3.1 - - - -
807C GLY* 2.6 43.5 - - - -
91Y ASN 2.9 13.4 + - - +
92Y ALA* 3.5 7.9 - - - +
93Y PHE 2.7 0.6 + - - -
94Y ALA* 1.3 76.9 - - - +
96Y PHE* 1.3 51.7 + - - +
97Y ASP 3.5 0.2 - - - -
98Y GLU 5.3 0.7 - - - -
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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