Contacts of the helix formed by residues 87 - 105 (chain G) in PDB entry 4D1Q
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 87 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G VAL* 1.3 75.9 - - - +
88G ALA* 1.3 59.4 + - - +
89G ASP* 2.9 15.5 - - - +
90G CYS* 3.3 16.0 + - - +
91G LYS* 2.8 29.2 + - - +
130H GLU* 5.6 0.3 + - - -
131H TYR* 2.7 26.6 + - - -
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Residues in contact with ALA 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G SER* 1.3 72.7 - - - +
89G ASP* 1.3 55.7 + - - +
91G LYS* 3.8 11.1 - - + +
92G LYS* 3.1 28.1 + - - +
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Residues in contact with ASP 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G SER* 4.0 11.9 - - - +
88G ALA* 1.3 78.0 - - - +
90G CYS* 1.3 60.8 + - - +
91G LYS 3.4 0.2 - - - -
92G LYS* 4.0 5.8 - - - +
93G GLU* 3.7 17.2 + - - +
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Residues in contact with CYS 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G VAL* 4.1 13.0 - - - -
87G SER* 3.3 18.8 + - - +
89G ASP* 1.3 77.1 - - - +
91G LYS* 1.3 65.5 + - - +
92G LYS 3.3 0.4 - - - -
93G GLU* 3.6 4.7 + - - +
94G ALA* 3.2 20.1 + - - +
123H PHE* 3.6 7.3 - - - -
127H VAL* 3.7 39.0 - - - -
130H GLU* 5.6 3.6 - - - +
131H TYR* 3.8 15.0 - - + +
140H LEU* 4.7 2.2 - - - -
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Residues in contact with LYS 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G VAL* 4.6 11.2 - - + +
87G SER 2.8 18.4 + - - +
88G ALA* 3.8 10.8 - - - +
90G CYS* 1.3 78.1 - - - +
92G LYS* 1.3 63.2 - - - +
94G ALA* 3.1 7.4 + - - +
95G ILE* 3.0 35.6 + - + +
139H GLU* 2.8 34.8 + - + +
140H LEU* 3.2 30.1 - - + +
142H PRO* 4.8 5.8 - - - -
5J T 3.9 16.0 + - - +
6J G 2.9 22.4 + - - -
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Residues in contact with LYS 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G ALA 3.1 17.6 + - - +
89G ASP* 4.1 7.9 - - - +
90G CYS 3.3 0.2 - - - -
91G LYS* 1.3 80.3 - - - +
93G GLU* 1.3 62.9 + - - +
94G ALA 3.2 1.0 + - - -
95G ILE* 3.2 24.5 + - + +
96G GLU* 3.3 26.3 + - + +
150H LYS* 6.3 2.5 - - + -
4J T 5.4 0.7 - - - -
5J T 3.9 21.1 - - - +
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Residues in contact with GLU 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G ASP 3.7 12.3 + - - +
90G CYS* 3.6 4.3 + - - +
91G LYS 3.4 0.6 - - - -
92G LYS* 1.3 79.5 - - - +
94G ALA* 1.3 59.8 + - - +
96G GLU* 3.8 19.6 - - + +
97G LYS* 3.3 46.0 + - + +
123H PHE* 3.3 25.2 - - + -
126H LYS* 3.2 26.4 + - - -
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Residues in contact with ALA 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G CYS 3.2 8.3 + - - +
91G LYS* 3.1 10.1 + - - +
93G GLU* 1.3 76.1 - - - +
95G ILE* 1.3 68.2 + - - +
96G GLU 3.1 0.2 - - - -
97G LYS* 3.5 1.0 + - - +
98G CYS* 3.2 27.2 + - - +
123H PHE* 3.2 30.5 - - + -
124H PHE* 4.5 5.8 - - + -
140H LEU* 3.9 25.1 - - + +
142H PRO* 4.7 5.4 - - + -
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Residues in contact with ILE 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G LYS* 3.0 22.6 + - + +
92G LYS* 3.5 17.9 - - + +
94G ALA* 1.3 77.8 - - - +
96G GLU* 1.3 68.9 + - + +
98G CYS 3.5 0.2 + - - -
99G ALA* 3.1 16.8 + - - +
142H PRO* 3.7 29.8 - - + +
146H THR* 3.5 22.2 - - + -
147H LEU* 3.6 5.3 - - + +
150H LYS* 3.7 34.8 - - + -
5J T 3.6 34.5 - - - +
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Residues in contact with GLU 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G LYS* 3.3 26.6 + - + +
93G GLU* 3.8 21.3 - - + +
94G ALA 3.1 0.6 - - - -
95G ILE* 1.3 80.2 - - + +
97G LYS* 1.3 60.1 + - + +
98G CYS 2.7 1.9 + - - -
99G ALA* 2.7 32.5 + - - +
100G GLN* 3.0 31.2 + - - +
150H LYS* 4.7 14.1 - - + -
154H ASP* 6.0 2.0 - - - +
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Residues in contact with LYS 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G GLU* 3.3 34.0 + - - +
94G ALA 3.5 2.9 + - - +
96G GLU* 1.3 80.4 + - + +
98G CYS* 1.3 55.5 + - - +
100G GLN* 3.8 29.1 + - - +
101G TRP* 3.1 25.5 + - - +
116H GLY 4.4 1.0 - - - +
119H ASP* 3.7 26.2 - - - +
120H MET* 3.7 16.1 - - + +
123H PHE* 3.5 42.0 - - + -
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Residues in contact with CYS 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G ALA 3.2 17.9 + - - +
96G GLU 2.7 5.3 + - - -
97G LYS* 1.3 72.3 - - - +
99G ALA* 1.3 57.7 + - - +
100G GLN 3.1 1.3 - - - -
101G TRP* 3.3 4.0 + - + +
102G VAL* 2.8 32.4 + - - +
112G VAL* 4.4 15.5 - - + -
117G PHE* 5.4 0.4 - - - -
120H MET* 3.6 27.8 - - - -
123H PHE* 6.1 0.2 - - - -
124H PHE* 4.0 22.0 - - - -
141H LEU* 5.1 1.6 - - - -
142H PRO* 4.3 12.1 - - + -
147H LEU* 3.7 22.2 - - + -
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Residues in contact with ALA 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G ILE 3.1 12.3 + - - +
96G GLU* 2.7 15.5 + - - +
98G CYS* 1.3 71.6 - - - +
100G GLN* 1.3 61.1 + - + +
102G VAL* 3.3 11.6 - - - +
103G VAL* 3.2 24.0 + - - +
147H LEU* 3.2 17.1 - - + +
150H LYS* 3.6 28.5 - - + -
151H VAL* 4.1 11.0 - - + +
154H ASP* 6.1 0.4 - - - +
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Residues in contact with GLN 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G GLU* 3.0 31.4 + - - +
97G LYS* 3.8 31.2 + - - +
99G ALA* 1.3 74.0 - - + +
101G TRP* 1.3 68.7 + - - +
102G VAL 2.9 1.1 - - - -
103G VAL* 2.7 9.6 + - - -
104G ARG* 2.7 47.7 + - - +
116H GLY* 5.6 0.9 - - - +
119H ASP* 6.1 0.3 - - - +
154H ASP* 5.4 3.5 + - - +
158H LYS* 5.9 1.6 - - - +
604H TYR* 3.9 33.3 + - + +
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Residues in contact with TRP 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G LYS 3.1 14.1 + - - +
98G CYS* 3.7 13.7 - - - +
100G GLN* 1.3 77.1 - - - +
102G VAL* 1.3 73.5 + - + +
105G ASP* 3.2 30.1 + - + +
106G CYS 4.1 0.2 + - - -
107G ARG* 4.1 23.1 - - + +
111G ALA* 3.6 33.4 - - + -
112G VAL* 4.1 10.1 - - + -
117G PHE* 4.0 29.6 - + - -
101H TRP* 3.8 25.8 - + - -
107H ARG* 6.1 0.2 - - - -
111H ALA 4.7 1.8 + - - -
116H GLY* 3.4 23.4 + - - +
117H PHE* 3.1 52.3 - + + +
120H MET* 3.8 17.5 - - - -
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Residues in contact with VAL 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G CYS 2.8 15.4 + - - +
99G ALA* 3.3 13.9 - - - +
100G GLN 2.9 1.0 + - - -
101G TRP* 1.3 89.5 - - + +
103G VAL* 1.3 65.7 + - + +
106G CYS* 3.2 4.7 - - - -
107G ARG* 2.9 38.3 + - + +
108G PRO 3.7 23.8 - - - +
109G PHE* 3.6 32.1 - - + +
112G VAL* 5.9 0.2 - - + -
147H LEU* 4.3 16.8 - - + -
151H VAL* 4.8 1.3 - - + -
597H LEU* 4.4 4.3 - - + +
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Residues in contact with VAL 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G ALA 3.2 6.6 + - - +
100G GLN* 2.7 21.0 + - - +
102G VAL* 1.3 73.0 - - + +
104G ARG* 1.3 78.8 + - + +
105G ASP 3.2 1.6 - - - -
106G CYS* 3.1 13.7 + - - +
151H VAL* 3.7 22.0 - - + -
597H LEU* 3.7 46.1 - - + +
600H LEU* 4.4 14.6 - - + -
601H ASN* 3.6 17.3 + - - +
604H TYR* 4.2 25.6 - - + -
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Residues in contact with ARG 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G GLN* 2.7 41.3 + - + +
103G VAL* 1.3 82.4 - - + +
105G ASP* 1.3 61.4 + - - +
115H SER* 3.1 35.0 + - - -
116H GLY* 3.8 22.2 - - - +
119H ASP* 3.5 29.9 + - - +
601H ASN* 3.9 15.8 + - - +
604H TYR* 4.2 34.2 - - + +
4K G 4.8 7.8 + - - -
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Residues in contact with ASP 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G TRP* 3.2 17.9 + - + +
104G ARG* 1.3 78.2 - - - +
106G CYS* 1.3 71.7 + - - +
107G ARG* 3.6 29.9 + - - +
111H ALA 4.1 2.8 - - - +
114H GLY* 3.1 32.8 - - - +
115H SER* 3.3 7.4 + - - -
116H GLY* 2.8 26.1 + - - -
117H PHE* 3.3 17.7 + - - +
4K G 5.3 8.0 - - - +
5K A 4.6 2.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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