Contacts of the helix formed by residues 91 - 105 (chain A) in PDB entry 4G1U
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A PRO 4.3 1.1 - - - -
88A GLY 4.9 0.7 - - - -
89A LEU 3.1 7.7 - - - +
90A LEU* 1.3 81.7 - - - +
92A ILE* 1.3 63.0 + - - +
93A SER 3.4 1.3 - - - -
94A SER* 4.0 3.8 - - - -
95A GLY 3.5 5.0 + - - -
130A ILE* 3.1 28.6 - - - +
152A GLY 4.6 0.2 - - - -
155A ILE* 3.5 10.4 - - - +
156A ASN* 3.3 25.8 - - - -
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Residues in contact with ILE 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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76A MET* 3.5 26.2 - - - -
80A PHE* 5.3 1.1 - - + -
87A PRO* 3.0 11.2 + - + +
90A LEU* 4.2 17.7 - - + -
91A GLY* 1.3 77.2 - - - +
93A SER* 1.3 66.4 + - - +
95A GLY* 3.3 2.6 + - - -
96A ALA* 3.0 21.7 + - - +
127A SER* 3.2 44.9 - - - +
130A ILE* 3.8 18.2 - - + +
131A SER* 3.1 30.7 - - - +
134A ILE* 4.9 1.3 - - + -
247A ILE* 3.9 14.1 - - + -
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Residues in contact with SER 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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69A LEU* 5.3 1.7 - - - +
87A PRO* 3.0 9.4 + - - +
88A GLY* 3.5 29.7 + - - -
92A ILE* 1.3 77.0 - - - +
94A SER* 1.3 57.7 + - - -
96A ALA* 3.1 4.2 + - - +
97A ALA* 2.9 29.8 + - - +
247A ILE* 3.7 6.8 - - - +
251A VAL* 3.5 28.4 - - - +
256A VAL* 4.1 20.0 - - - -
257A ILE 4.3 7.0 + - - -
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Residues in contact with SER 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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88A GLY* 5.9 0.7 - - - -
91A GLY* 3.9 6.5 + - - -
92A ILE 3.3 0.4 - - - -
93A SER* 1.3 78.7 - - - +
95A GLY* 1.3 56.1 - - - +
97A ALA* 3.7 6.2 - - - +
98A LEU* 2.9 31.0 + - - +
155A ILE* 4.5 2.7 - - - -
156A ASN* 3.0 32.1 + - - -
159A CYS* 3.9 28.8 - - - +
256A VAL* 4.3 13.7 - - - +
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Residues in contact with GLY 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 GLY 3.5 4.9 + - - -
92A ILE 3.3 4.7 + - - -
93A SER 3.2 0.6 - - - -
94A SER* 1.3 76.0 - - - +
96A ALA* 1.3 63.4 + - - +
98A LEU* 3.4 6.3 + - - +
99A CYS* 3.0 28.6 + - - +
126A GLY* 4.1 8.5 - - - -
130A ILE* 3.5 27.3 - - - +
159A CYS* 4.9 2.7 - - - -
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Residues in contact with ALA 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 ILE 3.0 13.2 + - - +
93A SER 3.5 7.2 - - - +
95A GLY* 1.3 75.7 - - - +
97A ALA* 1.3 56.2 + - - +
99A CYS* 3.2 5.7 + - - +
100A VAL* 2.9 28.9 + - - +
123A ALA* 3.2 35.3 - - + +
126A GLY* 4.0 2.7 - - - -
127A SER* 4.0 9.9 - - - +
247A ILE 4.9 1.6 - - - +
251A VAL* 3.7 23.1 - - + -
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Residues in contact with ALA 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 SER 2.9 15.9 + - - +
94A SER* 3.7 5.2 - - - +
96A ALA* 1.3 74.9 - - - +
98A LEU* 1.3 57.9 + - - +
100A VAL* 2.9 11.8 + - - +
101A GLY 2.9 24.1 + - - -
178A PHE* 3.3 8.6 - - + -
181A TRP* 5.0 7.2 - - + -
182A SER* 4.8 14.6 - - - -
251A VAL* 3.7 10.7 - - + +
255A GLY 4.9 0.4 - - - +
256A VAL* 3.9 20.4 - - + -
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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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94A SER 2.9 19.0 + - - +
95A GLY* 3.8 5.8 - - - +
96A ALA 3.4 0.2 - - - -
97A ALA* 1.3 75.6 - - - +
99A CYS* 1.3 59.0 + - - +
101A GLY* 3.4 3.5 + - - +
102A LEU* 2.9 44.4 + - + +
158A LEU* 5.2 8.1 - - + -
159A CYS* 3.7 32.3 - - + +
162A ALA* 4.5 21.3 - - + -
163A VAL* 4.9 11.2 - - + -
166A LEU* 6.4 2.0 - - + -
178A PHE* 5.1 3.6 - - + -
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Residues in contact with CYS 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 GLY 3.0 11.5 + - - +
96A ALA 3.2 6.9 + - - +
98A LEU* 1.3 75.0 - - - +
100A VAL* 1.3 63.9 + - - +
102A LEU* 3.3 14.9 + - - +
103A ILE* 3.0 30.7 + - + +
122A GLY* 3.2 24.0 - - - +
125A ILE* 4.5 8.5 - - - -
126A GLY* 3.4 29.4 - - - -
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Residues in contact with VAL 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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96A ALA 2.9 18.7 + - - +
97A ALA* 2.9 12.5 + - - +
99A CYS* 1.3 75.5 - - - +
101A GLY* 1.3 57.8 + - - +
103A ILE* 2.9 22.0 + - - +
104A ILE* 3.0 22.2 + - + +
119A HIS* 3.9 33.0 - - + +
123A ALA* 3.9 19.7 - - + +
178A PHE* 3.5 17.9 - - + -
181A TRP* 3.7 27.4 - - + -
252A ALA* 4.3 6.1 - - + -
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Residues in contact with GLY 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 ALA 2.9 10.7 + - - -
98A LEU* 3.7 4.5 - - - -
100A VAL* 1.3 75.5 - - - +
102A LEU* 1.3 58.1 + - - +
104A ILE* 3.1 7.6 + - - +
105A VAL* 3.0 38.8 + - - +
178A PHE* 3.3 27.0 - - - -
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Residues in contact with LEU 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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98A LEU* 2.9 31.7 + - + +
99A CYS* 3.6 16.6 - - - +
100A VAL 3.2 0.2 - - - -
101A GLY* 1.3 76.6 - - - +
103A ILE* 1.3 66.5 + - + +
104A ILE 3.4 0.2 - - - -
105A VAL* 4.3 10.3 - - + +
106A MET* 4.0 27.2 + - + +
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Residues in contact with ILE 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 CYS* 3.0 15.2 + - + +
100A VAL* 2.9 12.2 + - - +
102A LEU* 1.3 85.4 - - + +
104A ILE* 1.3 60.8 + - + +
106A MET* 4.0 13.6 - - - -
118A SER* 3.6 45.3 - - - +
119A HIS* 4.9 6.2 + - + +
122A GLY* 4.3 11.7 - - - -
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Residues in contact with ILE 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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100A VAL* 3.0 22.8 + - + +
101A GLY* 3.1 15.2 + - - +
103A ILE* 1.3 80.5 - - - +
105A VAL* 1.3 71.8 + - + +
106A MET 3.1 6.3 + - - -
119A HIS* 4.2 20.0 - - - +
174A GLN* 4.3 22.6 - - + +
175A LEU* 4.6 10.3 - - + -
178A PHE* 3.9 33.2 - - + -
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Residues in contact with VAL 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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101A GLY* 3.0 23.9 + - - +
102A LEU* 4.3 10.7 - - + +
104A ILE* 1.3 81.4 - - + +
106A MET* 1.3 65.6 + - + +
166A LEU* 5.1 12.3 - - + -
175A LEU* 4.9 14.8 - - + -
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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