Contacts of the helix formed by residues 87 - 106 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G TYR* 2.9 23.7 + - - -
86H VAL* 1.3 74.6 - - - +
88H ALA* 1.3 51.4 + - - +
89H ASP* 2.9 14.8 + - - +
90H CYS* 2.7 35.7 + - - +
91H LYS* 2.8 16.4 + - - +
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Residues in contact with ALA 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H VAL 3.9 1.0 + - - -
87H SER* 1.3 70.0 - - - +
89H ASP* 1.3 55.7 + - - +
90H CYS 3.4 0.2 - - - -
91H LYS* 3.9 11.0 - - - +
92H LYS* 3.2 34.2 + - - +
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Residues in contact with ASP 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H SER* 3.6 12.5 + - - +
88H ALA* 1.3 80.2 - - - +
90H CYS* 1.3 61.8 + - - +
92H LYS* 3.8 5.3 + - - +
93H GLU* 3.7 16.1 + - - +
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Residues in contact with CYS 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G PHE* 3.7 18.1 - - - -
127G VAL* 4.4 14.1 - - - -
130G GLU* 5.8 0.9 - - - +
131G TYR* 3.8 18.2 - - + +
140G LEU* 4.5 4.7 - - - -
86H VAL* 3.7 25.1 - - + -
87H SER* 2.7 23.1 + - - +
89H ASP* 1.3 74.3 + - - +
91H LYS* 1.3 64.1 + - - +
92H LYS 3.2 0.4 - - - -
93H GLU* 3.0 10.7 + - - +
94H ALA* 2.9 18.4 + - - +
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Residues in contact with LYS 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G GLU* 3.2 26.9 + - - +
140G LEU* 3.0 35.2 - - + +
142G PRO* 5.1 4.0 - - - -
1610G NA 4.0 1.8 - - - -
86H VAL* 4.3 8.7 - - + +
87H SER 2.8 13.4 + - - +
88H ALA* 3.9 12.1 - - - +
90H CYS* 1.3 76.2 - - - +
92H LYS* 1.3 58.0 + - - +
94H ALA* 3.0 8.4 + - + +
95H ILE* 3.0 39.1 + - + +
5L T 4.4 15.9 + - - +
6L G 3.5 22.5 + - - -
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Residues in contact with LYS 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G LYS* 6.0 2.9 - - - -
88H ALA* 3.2 18.6 + - - +
89H ASP* 3.9 7.4 - - - +
90H CYS 3.2 0.2 - - - -
91H LYS* 1.3 81.0 - - - +
93H GLU* 1.3 59.0 + - - +
95H ILE* 3.6 14.0 - - + +
96H GLU* 3.3 30.4 + - + +
4L T 5.0 2.9 - - - -
5L T 3.9 21.5 - - - +
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Residues in contact with GLU 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G PHE* 3.5 28.8 - - + +
126G LYS* 3.1 28.4 + - - +
89H ASP 3.7 8.2 + - - +
90H CYS* 3.0 8.7 + - - +
92H LYS* 1.3 76.3 - - - +
94H ALA* 1.3 64.8 + - - +
96H GLU* 3.9 14.8 - - - +
97H LYS* 3.1 46.9 + - + +
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Residues in contact with ALA 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G PHE* 3.4 24.2 - - + -
124G PHE* 5.1 2.7 - - + -
140G LEU* 4.0 28.3 - - + +
141G LEU* 5.8 0.2 - - + -
142G PRO* 5.2 5.4 - - + -
90H CYS 2.9 11.9 + - - +
91H LYS* 3.2 11.4 - - + +
93H GLU* 1.3 78.7 - - - +
95H ILE* 1.3 70.0 + - - +
96H GLU 3.2 0.2 + - - -
97H LYS* 3.3 1.2 + - - +
98H CYS* 3.2 26.2 + - - -
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Residues in contact with ILE 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G PRO* 4.2 18.6 - - + +
146G THR* 4.1 28.9 - - + -
147G LEU* 4.1 3.8 - - + +
150G LYS* 3.3 37.2 - - + -
91H LYS* 3.0 20.4 + - + +
92H LYS* 3.6 19.1 - - + +
94H ALA* 1.3 81.1 - - - +
96H GLU* 1.3 65.9 + - - +
98H CYS* 3.3 3.3 + - - +
99H ALA* 3.1 19.9 + - - +
5L T 3.1 35.9 - - - +
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Residues in contact with GLU 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G LYS* 3.8 29.9 + - + +
154G ASP* 5.3 5.1 - - - +
92H LYS* 3.3 20.8 + - + +
93H GLU* 3.9 15.6 - - + +
94H ALA 3.3 0.6 - - - -
95H ILE* 1.3 80.8 - - - +
97H LYS* 1.3 66.6 + - + +
98H CYS 3.0 0.3 + - - -
99H ALA* 3.1 2.4 + - - +
100H GLN* 2.9 46.9 + - - +
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Residues in contact with LYS 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G GLY 4.1 2.1 - - - +
119G ASP* 3.4 31.9 + - - +
120G MET* 3.6 17.8 + - + +
123G PHE* 3.2 43.5 - - + -
93H GLU* 3.1 34.6 + - + +
94H ALA 3.3 2.2 + - - +
96H GLU* 1.3 79.2 - - + +
98H CYS* 1.3 56.1 + - - +
100H GLN* 3.7 22.2 + - - +
101H TRP* 3.1 22.9 + - - +
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Residues in contact with CYS 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G MET* 2.9 32.5 - - + -
124G PHE* 4.2 11.9 - - - -
141G LEU* 4.6 2.7 - - - -
142G PRO* 4.3 16.8 - - + -
147G LEU* 3.9 20.9 - - + -
94H ALA 3.2 18.1 + - - -
95H ILE 3.6 6.1 - - - +
96H GLU 3.1 0.6 - - - -
97H LYS* 1.3 72.8 - - - +
99H ALA* 1.3 55.4 - - - +
100H GLN 3.0 1.3 - - - -
101H TRP* 2.6 28.5 + - + +
102H VAL* 2.8 18.4 + - - +
112H VAL* 5.1 5.6 - - + -
117H PHE* 5.7 0.2 - - - -
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Residues in contact with ALA 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G LEU* 3.9 19.1 - - + +
150G LYS* 3.7 30.3 - - + -
151G VAL* 4.0 13.5 - - + -
95H ILE 3.1 9.5 + - - +
96H GLU 3.1 6.7 + - - +
98H CYS* 1.3 77.7 - - - +
100H GLN* 1.3 58.7 + - + +
102H VAL* 3.2 5.2 + - - +
103H VAL* 2.8 36.2 + - - +
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Residues in contact with GLN 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G GLY* 5.4 1.3 - - - +
119G ASP* 6.1 0.9 - - - +
150G LYS* 6.3 0.2 - - + -
154G ASP* 5.6 2.0 + - - +
158G LYS* 6.1 0.8 - - - +
604G TYR* 3.7 33.5 + - + +
96H GLU* 2.9 48.3 + - - +
97H LYS* 3.7 23.5 + - - +
99H ALA* 1.3 76.0 - - + +
101H TRP* 1.3 56.5 + - - +
103H VAL* 3.0 9.7 + - - -
104H ARG* 2.6 50.1 + - - +
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Residues in contact with TRP 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G TRP* 3.8 23.1 - + - -
107G ARG* 5.7 0.4 - - - -
111G ALA 4.7 1.8 + - - -
116G GLY* 3.6 16.8 + - - +
117G PHE* 3.5 25.7 - + - +
120G MET* 3.5 21.8 - - + -
97H LYS 3.1 11.7 + - - +
98H CYS* 2.6 25.7 + - + +
100H GLN* 1.3 73.8 - - - +
102H VAL* 1.3 72.9 + - + +
105H ASP* 2.9 51.7 + - + +
107H ARG* 3.7 24.0 - - + +
111H ALA* 3.6 28.9 - - + -
112H VAL* 4.2 11.2 - - + -
117H PHE* 3.6 34.1 - + - -
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Residues in contact with VAL 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G LEU* 3.6 29.6 - - + -
586G ARG* 5.3 0.7 - - - +
597G LEU* 4.5 8.3 - - + +
98H CYS 2.8 11.3 + - - +
99H ALA* 3.3 10.5 - - - +
101H TRP* 1.3 84.4 - - + +
103H VAL* 1.3 64.2 + - + +
106H CYS* 2.9 27.4 + - - -
107H ARG* 3.0 37.3 + - + +
108H PRO 4.4 11.9 - - - +
109H PHE* 4.1 28.0 - - + +
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Residues in contact with VAL 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G VAL* 3.5 34.1 - - + -
597G LEU* 4.3 28.1 - - + +
600G LEU* 4.3 17.0 - - + -
601G ASN* 3.1 24.5 + - - +
604G TYR* 3.9 27.6 - - + -
99H ALA 2.8 19.8 + - - +
100H GLN* 3.5 7.9 - - - +
102H VAL* 1.3 75.4 - - + +
104H ARG* 1.3 66.5 + - + +
106H CYS* 3.8 6.6 + - - +
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Residues in contact with ARG 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G SER* 3.0 27.8 - - - -
116G GLY* 3.3 35.7 - - - +
119G ASP* 3.8 24.5 + - - +
601G ASN* 3.5 18.0 + - - +
604G TYR* 3.6 40.0 - - + +
100H GLN* 2.6 32.9 + - - +
103H VAL* 1.3 74.7 - - - +
105H ASP* 1.3 62.2 + - - +
106H CYS* 3.9 0.3 + - - +
4I G 4.4 10.7 + - - -
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Residues in contact with ASP 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G ALA 4.0 3.8 - - - +
114G GLY* 3.5 16.3 - - - -
115G SER* 3.5 7.3 + - - -
116G GLY 3.3 20.1 + - - -
117G PHE* 3.1 30.1 - - - +
101H TRP* 2.9 24.2 + - - +
104H ARG* 1.3 78.1 - - - +
106H CYS* 1.3 62.4 + - - +
107H ARG* 2.9 42.4 + - + +
4I G 5.0 9.6 + - - +
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Residues in contact with CYS 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577G LEU 5.0 1.1 - - - -
580G ASN* 3.9 27.8 - - - +
581G ILE* 3.9 29.4 - - - -
586G ARG* 4.7 6.3 + - - -
597G LEU* 5.0 6.1 - - - -
102H VAL 2.9 12.7 + - - -
103H VAL 3.8 4.8 + - - +
104H ARG 3.5 2.8 - - - +
105H ASP* 1.3 81.2 - - - +
107H ARG* 1.3 67.2 + - - +
108H PRO* 4.3 2.8 - - - +
585H LYS* 5.8 0.9 - - - +
4I G 5.6 9.0 - - - +
5I A 5.1 0.5 + - - -
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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