Contacts of the helix formed by residues 91 - 101 (chain A) in PDB entry 3U44
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A LEU* 4.4 4.9 - - - +
88A ARG* 3.0 25.1 + - - -
89A PRO 3.3 2.8 - - - +
90A GLY* 1.3 75.6 - - - +
92A LEU* 1.3 62.6 + - - +
93A HIS* 3.8 4.3 + - - +
94A ILE* 3.1 42.9 + - - +
95A ARG* 3.4 20.1 + - - +
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Residues in contact with LEU 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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90A GLY 3.5 5.9 + - - +
91A SER* 1.3 71.8 - - - +
93A HIS* 1.3 66.9 + - - +
95A ARG* 3.6 7.7 + - - +
96A ARG* 3.2 25.5 + - + +
247B HIS* 4.1 30.7 - - + +
249B LEU* 5.0 10.3 - - + +
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Residues in contact with HIS 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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48A ILE 2.9 29.1 + - - -
49A THR* 5.3 0.2 - - - -
54A PRO* 3.4 28.9 + - + +
55A ILE 3.8 6.7 + - - -
56A ASP* 3.1 14.5 + - - -
91A SER* 3.4 4.4 + - - +
92A LEU* 1.3 80.6 - - - +
94A ILE* 1.3 66.3 + - + +
96A ARG* 3.3 8.4 + - - +
97A GLN* 2.9 62.9 + - + +
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Residues in contact with ILE 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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49A THR* 4.2 23.6 - - + -
81A LEU* 3.7 32.9 - - + +
84A GLU* 3.9 31.4 - - + +
85A LEU* 3.8 15.3 - - + -
88A ARG* 4.6 13.7 - - - +
91A SER* 3.1 28.0 + - - +
93A HIS* 1.3 79.5 - - + +
95A ARG* 1.3 66.4 + - - +
97A GLN* 3.3 16.7 + - - +
98A LEU* 3.4 11.4 + - + +
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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 LEU* 4.8 13.4 - - + +
91A SER 3.4 16.4 + - - +
92A LEU* 3.9 11.0 - - - +
93A HIS 3.4 0.4 - - - -
94A ILE* 1.3 79.9 - - - +
96A ARG* 1.3 64.5 + - - +
98A LEU* 3.1 23.7 - - + +
99A SER* 3.6 3.3 + - - -
249B LEU* 3.9 42.1 + - + +
298B GLU* 4.0 20.6 + - - +
299B ALA* 5.4 0.6 - - - +
300B ARG* 2.9 54.0 - - + +
301B PRO* 5.6 0.4 - - - +
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Residues in contact with ARG 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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56A ASP* 4.9 9.4 + - - -
58A ASP* 5.7 1.2 + - - -
92A LEU* 3.2 19.4 + - + +
93A HIS* 3.5 9.6 - - - +
95A ARG* 1.3 77.2 - - - +
97A GLN* 1.3 60.4 + - - +
99A SER* 2.7 32.2 + - - -
100A LEU* 3.2 39.1 + - + +
103A ARG* 5.1 2.6 - - - +
248B GLU* 3.2 21.9 + - - +
249B LEU* 3.7 29.0 - - + +
644B ARG* 3.0 35.0 - - - +
648B LEU* 5.6 4.4 - - - +
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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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48A ILE* 3.5 15.8 - - + +
49A THR* 5.4 0.2 - - + -
56A ASP* 2.9 29.8 + - - -
57A VAL* 2.9 37.1 + - + +
81A LEU* 3.9 14.8 - - + -
93A HIS* 2.9 48.0 + - + +
94A ILE* 3.6 9.0 - - - +
95A ARG 3.3 0.2 - - - -
96A ARG* 1.3 78.9 - - - +
98A LEU* 1.3 55.4 + - - +
100A LEU* 2.7 31.6 + - - +
101A LEU* 2.9 18.4 + - - +
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Residues in contact with LEU 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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78A ALA* 3.8 22.2 - - + +
81A LEU* 3.5 35.6 - - + +
82A GLU* 3.0 33.4 - - - +
85A LEU* 4.7 11.4 - - + -
94A ILE* 3.4 5.4 + - + +
95A ARG* 3.1 18.1 + - + +
97A GLN* 1.3 78.9 - - - +
99A SER* 1.3 57.8 + - - +
101A LEU* 4.1 14.3 + - + +
102A ASN* 4.6 5.2 + - - -
300B ARG* 4.0 23.6 - - - +
687B ARG* 4.3 21.3 + - - +
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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 4.5 3.4 - - - -
96A ARG* 2.7 19.7 + - - -
98A LEU* 1.3 77.9 - - - +
100A LEU* 1.3 65.4 + - - +
101A LEU 3.4 1.1 - - - -
102A ASN* 4.1 7.5 + - - +
249B LEU* 5.1 8.1 - - - -
647B LEU* 3.7 26.9 + - - +
648B LEU* 3.9 24.2 - - - +
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Residues in contact with LEU 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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56A ASP* 3.7 24.5 - - + +
57A VAL* 4.0 12.6 - - + +
58A ASP* 4.2 19.0 - - + +
96A ARG* 3.5 38.8 - - + +
97A GLN* 2.7 38.9 + - - +
99A SER* 1.3 79.3 - - - +
101A LEU* 1.3 53.6 + - - +
102A ASN 3.1 3.4 - - - -
103A ARG* 2.9 22.5 + - - +
104A ALA* 2.7 36.4 + - - +
644B ARG* 5.7 3.1 - - + -
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Residues in contact with LEU 101 (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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57A VAL* 4.2 15.9 - - + -
74A LYS* 3.2 60.1 - - + +
77A ILE* 3.8 13.9 - - + -
78A ALA* 3.7 26.2 - - + +
81A LEU* 3.7 19.1 - - + -
97A GLN 2.9 28.0 + - - +
98A LEU* 4.1 11.7 - - + +
99A SER 3.4 1.0 - - - -
100A LEU* 1.3 77.6 - - - +
102A ASN* 1.3 64.8 + - - +
104A ALA* 3.7 13.0 + - + +
106A ILE* 6.2 0.9 - - + -
683B MET* 4.5 10.8 - - + -
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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