Contacts of the helix formed by residues 87 - 99 (chain A) in PDB entry 3LEZ
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 PHE 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A TYR* 3.5 32.6 - + + -
84A THR 3.2 22.7 + - - -
85A SER 3.1 1.6 - - - -
86A THR* 1.3 78.8 + - - +
88A LYS* 1.3 87.7 + - + +
89A PRO 3.4 0.2 - - - -
90A LEU* 2.9 20.1 + - + +
91A ALA* 3.0 26.4 + - + -
148A GLY* 4.1 15.7 - - - -
152A LEU* 3.8 36.1 - - + -
173A ILE* 5.2 2.2 - - + -
175A MET* 4.0 21.5 - - + -
179A GLU* 3.5 24.7 - - + -
182A LEU* 3.7 11.4 - - + -
199A MET* 4.5 6.5 - - - -
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Residues in contact with LYS 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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85A SER* 2.8 40.0 + - - +
87A PHE* 1.3 95.8 - - + +
89A PRO* 1.3 61.8 - - + +
91A ALA* 3.2 4.8 + - - +
92A VAL* 2.9 32.5 + - - +
139A ALA* 3.6 37.9 - - + +
140A ILE* 4.5 0.9 - - + -
143A SER* 3.3 16.6 + - - -
144A ASP 3.8 12.3 + - - -
145A ASN* 2.8 22.8 + - - +
148A GLY* 4.1 12.3 - - - -
151A LEU* 4.2 1.4 - - + +
179A GLU* 3.4 16.5 + - - -
247A LYS* 4.0 8.3 - - - -
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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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86A THR 3.3 16.2 - - - +
88A LYS* 1.3 89.9 - - + +
90A LEU* 1.3 59.1 + - - +
91A ALA 3.4 0.2 - - - -
92A VAL* 3.7 1.7 - - + +
93A GLY* 2.8 24.6 + - - -
140A ILE* 3.9 18.4 - - + -
203A LEU* 4.3 11.3 - - + +
206A TYR* 4.9 1.4 - - - +
220A LEU* 4.1 10.7 - - + +
224A LEU* 4.0 20.9 - - + -
247A LYS* 3.5 35.9 - - + -
259A ILE* 4.3 11.7 - - + -
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Residues in contact with LEU 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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86A THR 4.2 7.2 - - - +
87A PHE* 2.9 13.0 + - + +
89A PRO* 1.3 75.8 - - - +
91A ALA* 1.3 60.9 + - - +
93A GLY* 3.3 1.0 + - - -
94A ALA* 2.9 28.2 + - - +
161A LEU* 5.1 2.0 - - + -
165A LEU* 4.4 18.8 - - + +
170A ASP* 5.0 0.9 - - - +
173A ILE* 4.2 15.9 - - + -
199A MET* 3.6 33.2 - - + +
202A THR* 3.9 23.8 - - + -
203A LEU* 3.9 40.8 - - + +
206A TYR* 3.8 12.1 - - + -
259A ILE* 4.9 3.6 - - + -
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Residues in contact with ALA 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 PHE* 3.0 23.7 + - + +
88A LYS 3.6 7.0 - - - +
90A LEU* 1.3 74.3 - - - +
92A VAL* 1.3 59.6 + - - +
94A ALA* 3.2 3.3 + - - +
95A VAL* 2.9 33.7 + - - +
151A LEU* 4.0 26.0 - - + +
152A LEU* 5.0 0.2 - - + -
155A MET* 4.5 1.2 - - + +
161A LEU* 3.8 29.5 - - + +
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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
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88A LYS 2.9 21.1 + - - +
89A PRO 3.7 4.7 - - - +
91A ALA* 1.3 73.3 - - - +
93A GLY* 1.3 66.4 + - - +
95A VAL* 3.1 8.5 + - + +
96A LEU* 2.9 43.4 + - + +
136A ALA* 3.5 36.6 - - + -
140A ILE* 3.7 20.9 - - + -
151A LEU* 3.7 16.4 - - + -
220A LEU* 4.0 11.9 - - + -
223A MET* 4.6 3.6 - - + -
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Residues in contact with GLY 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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89A PRO 2.8 16.2 + - - -
90A LEU 3.3 4.0 + - - -
92A VAL* 1.3 76.5 - - - +
94A ALA* 1.3 55.9 + - - +
96A LEU* 3.2 1.8 + - - -
97A GLN* 2.8 30.0 + - - +
206A TYR* 3.3 29.2 - - - -
212A LEU* 3.4 7.0 - - - +
220A LEU* 4.3 10.5 - - - +
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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 LEU 2.9 10.4 + - - +
91A ALA 3.2 2.9 + - - +
93A GLY* 1.3 75.0 - - - +
95A VAL* 1.3 57.4 + - - +
97A GLN* 3.3 4.8 + - - +
98A THR* 2.8 35.3 + - - +
155A MET* 3.7 13.5 - - + -
161A LEU* 3.4 33.4 - - + -
164A ILE* 4.3 6.7 - - + -
165A LEU* 4.8 0.2 - - + -
206A TYR* 3.4 17.8 + - - +
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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 ALA 2.9 16.4 + - - +
92A VAL* 3.4 11.4 - - + +
94A ALA* 1.3 77.0 - - - +
96A LEU* 1.3 60.3 + - + +
98A THR* 4.2 0.9 - - - -
99A LYS* 3.0 41.7 + - + +
104A LEU* 3.6 23.3 - - + +
132A LEU* 4.1 15.5 - - + +
151A LEU* 4.1 24.2 - - + +
154A ALA* 4.8 9.0 - - + -
155A MET* 3.7 25.4 - - + -
216A ARG* 4.1 0.3 + - - -
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Residues in contact with LEU 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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92A VAL* 2.9 39.4 + - + +
93A GLY 3.7 3.6 - - - +
95A VAL* 1.3 78.5 - - + +
97A GLN* 1.3 58.9 + - - +
104A LEU* 3.9 28.0 - - + -
133A VAL* 5.2 6.1 - - + -
212A LEU* 3.6 18.4 - - + +
213A ASP 5.5 0.7 + - - -
216A ARG* 2.9 65.6 + - + +
219A VAL* 4.8 11.7 - - + -
220A LEU* 3.8 18.2 - - + +
223A MET* 6.2 0.2 - - + -
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Residues in contact with GLN 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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93A GLY 2.8 13.2 + - - +
94A ALA* 3.5 4.1 - - - +
96A LEU* 1.3 80.1 - - - +
98A THR* 1.3 70.1 + - + +
99A LYS 3.8 1.1 - - - +
164A ILE* 3.8 18.6 - - - +
168A ILE* 3.7 17.3 - - - +
206A TYR* 2.8 31.9 + - - -
211A VAL* 3.7 24.4 - - + +
212A LEU* 3.6 12.6 - - + +
216A ARG* 5.0 0.4 + - - -
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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 ALA 2.8 20.7 + - - +
95A VAL* 4.0 0.9 + - - -
97A GLN* 1.3 99.7 - - + +
99A LYS* 1.3 67.4 + - - +
100A SER 4.1 0.7 + - - -
103A GLU* 4.3 2.6 - - - +
155A MET* 3.5 27.4 - - + +
164A ILE* 4.4 13.5 - - + -
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Residues in contact with LYS 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* 3.0 31.6 + - + +
97A GLN 5.0 0.9 - - - +
98A THR* 1.3 85.6 - - - +
100A SER* 1.3 61.3 + - - +
103A GLU* 3.3 28.0 + - + +
104A LEU* 3.9 14.6 - - + -
132A LEU* 4.3 16.1 - - + +
154A ALA* 2.8 35.6 + - - +
155A MET* 4.4 11.2 - - - -
216A ARG* 2.7 27.9 + - - -
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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