Contacts of the helix formed by residues 90 - 105 (chain A) in PDB entry 4UTX
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 ASP 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ALA 2.7 15.9 + - - +
89A ARG* 1.3 86.8 - - + +
91A PRO* 1.3 67.3 - - - +
92A SER* 3.8 7.6 + - - -
93A LEU* 3.1 42.1 + - + +
94A VAL* 3.1 14.9 + - + +
192A GLU* 3.4 15.8 - - - +
194A ARG* 4.3 23.3 + - - +
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Residues in contact with PRO 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 46.2 - - + +
88A SER 3.9 5.6 - - - +
89A ARG 3.7 4.9 - - - +
90A ASP* 1.3 84.8 - - - +
92A SER* 1.3 65.7 + - - +
94A VAL* 4.1 0.6 - - - +
95A TRP* 2.9 29.5 + - - +
197A VAL* 4.2 21.3 - - + -
200A LEU* 3.8 13.2 - - + -
211A LEU* 4.7 5.4 - - + -
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASP* 3.3 7.1 - - - -
91A PRO* 1.3 80.0 - - - +
93A LEU* 1.3 54.3 + - - +
95A TRP* 3.3 1.7 + - - +
96A GLU* 2.7 37.8 + - - +
180A LEU* 5.0 0.3 - - - +
193A ALA* 4.0 4.0 - - - +
194A ARG* 3.3 16.4 + - - -
195A ILE* 3.0 50.0 + - - +
200A LEU* 3.7 14.9 - - - +
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Residues in contact with LEU 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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73A TRP* 3.6 16.8 - - + -
74A ARG* 3.5 28.0 - - - +
76A TRP* 3.7 33.9 - - + -
81A LEU* 4.3 16.1 - - + +
90A ASP* 3.1 34.1 + - + +
92A SER* 1.3 82.4 - - - +
94A VAL* 1.3 63.8 + - + +
96A GLU* 3.2 11.0 + - - +
97A PHE* 3.1 20.4 + - - +
192A GLU* 3.7 15.9 - - + +
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Residues in contact with VAL 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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81A LEU* 3.8 25.6 - - + +
86A ALA* 3.6 36.8 - - + +
87A PHE* 3.7 27.6 - - + +
90A ASP* 3.1 16.3 + - + +
91A PRO 4.1 0.2 - - - +
92A SER 3.3 0.2 - - - -
93A LEU* 1.3 76.0 - - + +
95A TRP* 1.3 62.3 + - - +
97A PHE* 3.0 12.6 + - + +
98A TYR* 2.9 41.5 + - + -
214A PRO* 5.6 0.2 - - + -
218A TRP* 4.1 6.7 - - + -
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Residues in contact with TRP 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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87A PHE* 3.6 15.5 - + - -
91A PRO 2.9 23.7 + - - +
92A SER 3.7 2.2 - - - +
94A VAL* 1.3 73.8 - - - +
96A GLU* 1.3 66.6 + - - +
98A TYR* 4.2 12.8 - - + +
99A HIS* 2.7 30.0 + - - +
102A ARG* 4.6 10.5 - - - -
159A LYS 5.8 0.2 - - - -
160A THR* 4.7 5.8 - - + -
176A ILE* 3.6 31.9 - - + -
180A LEU* 4.2 11.0 - - + -
200A LEU* 4.0 31.0 - - + -
201A PRO* 4.0 22.4 - - + +
211A LEU* 4.6 1.8 - - - +
212A LEU* 2.9 32.7 + - + -
213A ARG* 3.7 15.7 - - - -
214A PRO* 3.8 26.2 - - + -
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Residues in contact with GLU 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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73A TRP* 3.9 10.5 - - + -
74A ARG* 2.7 38.4 + - - -
92A SER* 2.7 21.9 + - - +
93A LEU* 3.4 18.2 - - - +
95A TRP* 1.3 73.5 - - - +
97A PHE* 1.3 62.2 - - - +
99A HIS* 3.2 2.6 + - - +
100A TYR* 3.0 17.8 + - - +
180A LEU* 4.1 16.1 - - + +
183A LYS* 3.9 3.5 - - + +
184A GLY* 3.3 24.6 + - - +
190A THR* 5.1 0.2 - - - +
191A LYS 4.3 2.1 - - - +
192A GLU* 3.7 2.8 - - - +
193A ALA* 3.0 46.0 + - + +
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Residues in contact with PHE 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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66A PHE* 4.0 24.0 - + + -
73A TRP* 3.6 48.2 - + + -
78A ALA* 4.5 18.6 - - + -
81A LEU* 4.0 28.7 - - + -
82A ALA* 4.9 3.6 - - + -
93A LEU 3.1 10.7 + - - +
94A VAL* 3.0 13.4 + - + +
96A GLU* 1.3 74.9 - - - +
98A TYR* 1.3 83.5 + + - +
100A TYR* 3.3 6.6 - - - +
101A ARG* 3.2 56.9 + - - +
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Residues in contact with TYR 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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82A ALA* 3.5 7.9 - - - +
94A VAL* 2.9 32.6 + - + +
95A TRP* 4.1 12.1 - - + +
97A PHE* 1.3 87.3 - + - +
99A HIS* 1.3 60.3 + - - +
101A ARG* 3.2 29.3 + - - +
102A ARG* 2.9 37.0 + - - +
138A ILE* 4.6 0.2 - - + -
157A LEU* 3.5 27.1 - - + -
214A PRO* 3.8 26.9 - - + -
216A VAL* 3.9 9.8 - - + +
218A TRP* 2.9 34.3 + + - -
1004C 3NP 2.4 27.6 + - - -
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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 TRP* 2.7 22.9 + - - +
96A GLU 3.4 4.5 - - - +
98A TYR* 1.3 68.7 - - - +
100A TYR* 1.3 65.5 + - - +
102A ARG* 3.2 14.5 + - - +
103A GLU* 2.9 56.1 + - + +
175A PRO* 3.6 25.3 - - + +
176A ILE* 4.5 12.2 + - + +
180A LEU* 3.1 43.2 + - + -
182A GLY* 4.0 10.3 + - - -
183A LYS* 3.5 24.3 + - + -
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Residues in contact with TYR 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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64A PRO* 5.1 2.6 - - + +
66A PHE* 4.1 25.1 - + - -
73A TRP* 3.8 20.6 - + - +
96A GLU 3.0 7.4 + - - +
97A PHE 3.3 9.0 - - - +
99A HIS* 1.3 81.2 - - - +
101A ARG* 1.3 55.6 + - + +
103A GLU* 3.0 7.3 + - + +
104A VAL* 2.7 62.6 + - + +
183A LYS 5.2 1.6 - - - -
184A GLY* 3.4 29.2 - - - +
185A ALA* 4.9 0.7 - - - -
186A PRO* 3.7 32.1 - - + +
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Residues in contact with ARG 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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63A VAL* 6.1 1.6 - - - +
64A PRO* 4.5 12.9 + - + +
65A THR* 5.2 3.4 + - - +
66A PHE* 3.6 38.7 - - + -
97A PHE* 3.2 35.8 + - + +
98A TYR* 3.2 39.2 - - - +
99A HIS 3.2 0.4 - - - -
100A TYR* 1.3 79.1 - - + +
102A ARG* 1.3 64.3 + - - +
104A VAL* 3.5 13.6 + - - +
105A MET* 3.3 18.9 - - - +
138A ILE* 3.9 20.1 - - - +
157A LEU* 4.0 18.0 - - + +
1300A EDO 4.5 8.9 + - - -
1004C 3NP 3.1 29.4 + - - -
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Residues in contact with ARG 102 (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 TRP* 4.6 13.2 - - - -
98A TYR* 2.9 25.2 + - - +
99A HIS* 3.3 13.2 + - - +
101A ARG* 1.3 78.8 - - - +
103A GLU* 1.3 69.3 + - - +
105A MET* 3.3 16.8 + - - +
106A ARG* 4.2 5.0 + - - +
157A LEU* 2.9 36.8 + - + +
158A PHE* 3.3 31.7 - - + +
159A LYS 5.6 0.2 + - - -
160A THR* 5.6 2.0 - - - +
171A ASN* 2.9 44.3 + - - -
172A HIS 3.8 1.6 - - - -
173A LYS 3.1 24.4 + - - +
176A ILE* 3.6 29.5 - - - +
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Residues in contact with GLU 103 (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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99A HIS* 2.9 55.3 + - + +
100A TYR* 3.8 5.4 - - + +
102A ARG* 1.3 73.8 + - - +
104A VAL* 1.3 65.9 + - - +
105A MET 2.7 6.9 + - - -
106A ARG* 2.9 41.5 + - - +
107A SER 4.3 0.5 + - - -
173A LYS 4.3 3.8 - - - +
174A SER* 2.6 39.5 + - - -
175A PRO* 4.4 0.9 - - - +
176A ILE 5.1 0.2 + - - -
298B GLU* 5.0 3.5 - - - +
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Residues in contact with VAL 104 (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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63A VAL* 5.3 0.7 - - + -
64A PRO* 4.2 25.8 - - + -
100A TYR* 2.7 66.3 + - + +
101A ARG* 3.6 14.6 - - - +
103A GLU* 1.3 71.3 - - - +
105A MET* 1.3 72.4 + - - +
106A ARG 3.3 0.2 - - - -
107A SER* 3.2 20.9 + - - +
108A LYS* 3.3 20.0 - - + +
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Residues in contact with MET 105 (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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63A VAL* 4.0 24.0 - - + -
101A ARG 3.3 17.0 - - - +
102A ARG 3.4 9.6 - - - +
103A GLU 2.7 1.6 + - - -
104A VAL* 1.3 79.1 - - - +
106A ARG* 1.3 66.6 + - + +
107A SER 3.0 4.1 + - - -
108A LYS* 3.0 27.1 + - + +
139A ASP* 3.6 38.8 - - + +
141A LEU* 3.8 17.3 - - + -
144A ARG* 3.2 27.0 + - - +
157A LEU* 4.4 7.0 - - + -
158A PHE* 3.9 22.7 - - + -
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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