Contacts of the helix formed by residues 94 - 103 (chain A) in PDB entry 4Y2H
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 GLY 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ALA* 2.7 31.7 + - - -
92A GLY 3.1 1.6 + - - -
93A THR* 1.3 71.1 - - - +
95A ILE* 1.3 63.6 + - - +
96A LEU 3.4 2.7 - - - -
97A SER* 3.3 11.4 + - - -
98A ILE* 3.1 29.0 + - - +
110A ALA* 5.5 1.3 - - - -
120A ALA* 4.0 11.7 - - - -
124A VAL* 5.2 3.5 - - - +
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Residues in contact with ILE 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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61A ILE* 4.1 20.6 - - + -
66A ARG* 4.8 2.7 - - - +
67A THR* 4.1 14.6 - - + -
91A ALA 4.2 0.6 + - - -
93A THR* 3.4 14.9 + - - +
94A GLY* 1.3 76.9 - - - +
96A LEU* 1.3 66.8 + - + +
98A ILE* 3.2 11.5 + - - +
99A PHE* 3.1 53.7 + - + -
401A SAH 3.6 28.5 - - - +
211B VAL* 4.4 12.3 - - + -
215B TYR* 4.4 5.8 - - + -
217B VAL* 4.4 10.3 - - + -
219B MET* 4.3 14.3 - - - +
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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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66A ARG* 5.1 4.0 - - - +
67A THR* 5.4 2.2 - - + -
70A TYR* 3.6 40.2 - - + -
74A ILE* 4.0 7.1 - - + +
88A ASP* 3.9 14.3 + - - +
94A GLY 3.4 0.4 - - - -
95A ILE* 1.3 77.2 - - + +
97A SER* 1.3 61.8 + - - +
99A PHE* 3.2 23.6 + - + +
100A CYS* 2.9 32.3 + - - -
153A VAL* 4.6 8.3 - - + -
154A SER 4.6 0.2 - - - -
155A GLU* 3.9 22.7 - - + +
401A SAH 3.4 42.7 + - - +
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Residues in contact with SER 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASP* 2.6 37.3 + - - +
91A ALA* 3.9 0.9 - - - +
94A GLY* 3.3 11.0 + - - -
96A LEU* 1.3 75.7 - - - +
98A ILE* 1.3 57.0 + - - +
100A CYS* 3.2 6.8 + - - +
101A ALA* 3.0 26.3 + - - +
108A VAL* 3.8 22.2 - - - +
110A ALA* 3.2 15.2 - - - +
133A VAL* 3.8 20.2 - - - +
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Residues in contact with ILE 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 GLY 3.1 17.5 + - - +
95A ILE 3.6 6.7 - - - +
96A LEU 3.1 0.6 - - - -
97A SER* 1.3 75.2 - - - +
99A PHE* 1.3 58.6 + - - +
101A ALA* 3.1 6.0 + - - +
102A GLN* 2.8 41.1 + - - +
123A VAL* 3.7 30.1 - - + -
124A VAL* 4.0 26.2 - - + -
127A ASN* 4.3 8.5 - - - +
129A LEU* 3.7 25.8 - - + -
133A VAL* 4.6 3.4 - - + -
217B VAL* 3.7 32.5 - - + -
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Residues in contact with PHE 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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67A THR* 4.0 21.3 - - + -
71A ARG* 3.3 42.4 - - + +
74A ILE* 3.6 22.8 - - + +
75A LEU* 4.0 6.2 - - + +
95A ILE* 3.1 42.9 + - + -
96A LEU* 3.4 24.7 - - + +
98A ILE* 1.3 76.6 - - - +
100A CYS* 1.3 62.9 + - - +
102A GLN* 3.3 16.3 + - - +
103A ALA* 3.0 22.7 + - - +
215B TYR* 3.7 25.4 - - + -
217B VAL* 3.8 13.2 - - + -
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Residues in contact with CYS 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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74A ILE* 3.9 24.9 - - - -
81A LEU* 4.6 9.2 - - + +
86A VAL* 4.0 18.6 - - + -
96A LEU 2.9 15.6 + - - +
97A SER* 3.4 10.5 - - - +
98A ILE 3.2 0.2 - - - -
99A PHE* 1.3 76.3 - - - +
101A ALA* 1.3 61.7 + - - +
103A ALA* 3.0 15.6 + - - +
105A ALA* 3.3 16.4 + - - +
108A VAL* 3.9 15.0 - - + -
153A VAL* 3.9 26.5 - - - -
185A LEU* 5.7 0.7 - - - -
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Residues in contact with ALA 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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97A SER 3.0 14.0 + - - +
98A ILE* 3.1 7.4 + - - +
100A CYS* 1.3 72.5 - - - +
102A GLN* 1.3 60.7 + - - +
104A GLY 2.8 18.2 + - - -
105A ALA* 4.2 7.4 - - - +
108A VAL* 4.2 3.3 - - + +
129A LEU* 4.4 13.2 - - + -
132A ARG* 2.9 37.1 + - + +
133A VAL* 3.9 20.6 - - + -
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Residues in contact with GLN 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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71A ARG* 5.9 0.5 - - - -
75A LEU* 4.6 9.6 - - + +
98A ILE* 2.8 35.3 + - + +
99A PHE* 3.7 26.1 - - - +
101A ALA* 1.3 74.5 - - - +
103A ALA* 1.3 59.3 + - - +
104A GLY 3.2 0.9 + - - -
127A ASN* 5.7 1.2 + - - -
129A LEU* 5.1 7.8 - - + +
215B TYR 4.7 2.9 - - - +
216B GLY* 3.1 26.6 + - - +
217B VAL* 4.2 1.5 - - - +
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Residues in contact with ALA 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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74A ILE* 4.0 19.3 - - + +
75A LEU* 3.8 20.6 - - + +
78A TRP* 4.0 15.8 - - + +
81A LEU* 4.4 9.9 - - + -
82A ARG* 3.4 20.6 + - - +
99A PHE 3.0 12.5 + - - +
100A CYS* 3.3 11.4 - - - +
101A ALA 3.0 0.8 - - - -
102A GLN* 1.3 76.2 - - - +
104A GLY* 1.3 58.1 + - - +
105A ALA 3.7 0.2 - - - -
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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