Contacts of the helix formed by residues 100 - 118 (chain C) in PDB entry 1P4D
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 LYS 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C VAL 5.0 6.0 + - - -
26C LEU* 3.7 20.9 + - - +
27C GLY* 5.7 0.6 - - - -
94C ALA 4.6 4.3 - - - +
95C MET* 5.8 4.7 - - - +
98C GLY* 2.6 26.9 + - - +
99C ASP* 1.3 70.8 - - - +
101C ARG* 1.3 64.8 + - - +
102C LEU 3.2 2.0 - - - -
103C ILE* 3.3 41.1 + - + +
104C ASP* 3.6 9.8 + - - +
292C ARG* 5.1 0.2 - - - +
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Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ASP* 2.8 36.8 + - - +
100C LYS* 1.3 77.2 - - - +
102C LEU* 1.3 55.8 + - - +
103C ILE 3.0 0.4 - - - -
104C ASP* 2.8 42.4 + - - +
105C ALA 3.1 4.3 + - - -
211C LEU* 3.4 56.3 + - + +
213C TYR* 4.0 8.5 + - - -
292C ARG* 3.4 21.9 - - - +
295C ALA* 5.2 1.0 - - - +
296C ASP* 3.5 23.7 + - - -
603C EDO 3.6 7.8 - - - +
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C VAL* 3.9 17.5 - - + +
93C MET* 3.5 23.8 - - + +
94C ALA* 3.2 39.0 - - + +
99C ASP* 3.8 16.4 - - + +
101C ARG* 1.3 79.3 - - - +
103C ILE* 1.3 56.4 + - - +
105C ALA* 3.1 8.4 + - - +
106C HIS* 2.7 29.6 + - - +
156C LEU* 5.1 1.3 - - - +
204C LEU* 4.4 2.3 - - - +
208C VAL* 4.0 22.9 - - + -
211C LEU* 3.9 11.9 - - + -
213C TYR* 3.8 23.6 - - + -
226C MET* 4.6 3.6 - - + -
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Residues in contact with ILE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 3.5 37.9 - - + +
94C ALA* 4.2 17.5 - - + -
95C MET* 5.8 0.7 - - - -
100C LYS* 3.4 45.1 - - + +
101C ARG 3.0 0.4 - - - -
102C LEU* 1.3 78.3 - - - +
104C ASP* 1.3 63.0 + - - +
106C HIS* 3.3 5.9 + - - +
107C ASN* 2.9 48.3 + - - +
145C ASN* 4.9 4.0 - - - +
156C LEU* 4.3 10.1 - - + -
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Residues in contact with ASP 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C LYS 3.6 6.2 - - - +
101C ARG* 2.8 28.7 + - - +
103C ILE* 1.3 79.6 - - - +
105C ALA* 1.3 61.6 + - - +
107C ASN* 3.8 7.3 - - - +
108C GLN* 3.0 36.5 + - - +
603C EDO 3.6 15.5 + - - +
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG 3.1 4.8 + - - +
102C LEU* 3.1 15.6 + - - +
104C ASP* 1.3 74.4 - - - +
106C HIS* 1.3 68.7 + - - +
108C GLN* 2.8 12.5 + - - -
109C ALA* 2.8 11.4 + - - +
204C LEU* 3.8 12.3 - - + -
207C GLN* 3.1 45.7 - - + +
208C VAL* 4.9 4.9 - - + +
211C LEU* 5.0 2.0 - - + -
603C EDO 3.5 7.7 - - - -
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Residues in contact with HIS 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C PHE 3.7 3.4 + - - -
86C ALA* 3.7 10.1 - - + -
90C VAL* 6.1 0.9 - - + -
102C LEU 2.7 15.7 + - - +
103C ILE* 3.4 8.3 - - - +
105C ALA* 1.3 71.7 - - - +
107C ASN* 1.3 68.7 + - - +
109C ALA* 2.8 22.3 + - - +
110C VAL* 2.9 28.1 + - + +
145C ASN* 5.0 0.2 - - - -
156C LEU* 3.6 32.6 + - + +
157C HIS* 3.5 20.3 - - - -
158C THR* 2.8 33.0 + - - -
200C TYR* 3.2 22.0 + - - -
204C LEU* 3.4 15.4 - - + +
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Residues in contact with ASN 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLY* 5.8 2.8 - - - -
32C ARG* 3.8 19.1 + - - +
103C ILE* 2.9 31.8 + - - +
104C ASP* 3.8 8.0 - - - +
106C HIS* 1.3 88.0 + - - +
108C GLN* 1.3 54.3 + - + +
110C VAL* 3.5 4.8 + - - +
111C ASP* 2.6 40.7 + - - +
145C ASN* 2.8 28.9 + - - +
156C LEU* 5.9 0.4 - - - +
158C THR* 4.2 1.6 + - - -
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Residues in contact with GLN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ASP* 3.0 22.6 + - - +
105C ALA 2.8 2.3 + - - +
107C ASN* 1.3 74.6 - - + +
109C ALA* 1.3 63.6 + - - +
111C ASP* 3.7 10.8 - - - +
112C PHE* 3.3 20.4 + - - +
115C ARG* 5.4 0.9 + - - -
203C LYS* 4.1 7.9 - - + +
207C GLN* 2.8 37.3 + - - +
603C EDO 3.7 15.4 + - - -
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ALA 2.8 9.6 + - - +
106C HIS 2.8 11.1 + - - +
108C GLN* 1.3 77.8 - - - +
110C VAL* 1.3 65.6 + - - +
112C PHE* 3.0 15.2 + - - +
113C ALA* 3.0 13.7 + - - +
200C TYR* 3.4 38.2 - - + +
203C LYS* 3.8 10.3 - - + -
204C LEU* 3.9 17.9 - - + +
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ARG* 4.8 1.6 - - - +
84C PHE* 4.1 14.4 - - + -
106C HIS* 2.9 42.1 + - + +
107C ASN* 3.7 8.5 - - - +
109C ALA* 1.3 76.5 - - - +
111C ASP* 1.3 59.7 + - - +
113C ALA* 3.1 4.9 + - - +
114C VAL* 2.8 39.2 + - + +
143C LEU* 3.6 28.0 - - + -
158C THR* 3.7 21.3 - - + +
160C ALA* 5.2 0.4 - - + -
200C TYR* 3.8 14.1 - - + -
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Residues in contact with ASP 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ARG* 3.5 25.9 + - - -
34C ALA* 5.4 4.7 - - - +
107C ASN* 2.6 28.5 + - - +
108C GLN* 3.7 11.9 - - - +
110C VAL* 1.3 76.4 - - - +
112C PHE* 1.3 59.7 - - - +
114C VAL* 4.0 4.8 - - - +
115C ARG* 3.0 46.2 + - + +
143C LEU* 4.3 5.2 - - - +
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Residues in contact with PHE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C GLN 3.3 11.7 + - - +
109C ALA 3.0 8.6 + - - +
111C ASP* 1.3 81.4 - - - +
113C ALA* 1.3 59.7 + - - +
115C ARG* 3.5 19.2 + - - +
116C GLN* 2.6 57.4 + - + +
199C LEU* 3.0 50.3 - - + -
203C LYS* 3.8 35.9 - - + -
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Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C PHE* 3.7 27.6 - - + -
109C ALA 3.0 11.0 + - - +
110C VAL 3.6 6.1 - - - +
112C PHE* 1.3 73.7 - - - +
114C VAL* 1.3 58.4 + - - +
115C ARG 3.0 1.8 - - - -
116C GLN* 2.6 27.7 + - - +
117C VAL* 2.9 15.9 + - + +
196C PHE* 5.4 0.4 - - + -
199C LEU* 3.6 29.8 - - + -
200C TYR* 4.1 5.8 - - + -
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ALA* 5.0 9.0 - - + -
35C GLY* 5.6 0.9 - - - +
82C LEU* 5.8 1.8 - - + -
84C PHE* 4.1 9.2 - - + -
110C VAL* 2.8 35.2 + - + +
111C ASP* 4.1 5.2 - - - +
113C ALA* 1.3 72.7 - - - +
115C ARG* 1.3 61.1 + - + +
117C VAL* 3.5 11.2 + - + +
118C GLU* 2.9 26.9 + - - +
141C MET* 3.2 33.9 - - + +
143C LEU* 4.5 8.5 - - + -
160C ALA* 3.8 28.3 - - + -
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Residues in contact with ARG 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ARG* 5.2 4.6 + - - +
108C GLN 5.4 1.0 + - - -
111C ASP* 3.0 30.4 + - - +
112C PHE* 3.9 23.5 - - - +
113C ALA 2.9 1.0 + - - -
114C VAL* 1.3 80.7 - - + +
116C GLN* 1.3 79.2 + - - +
118C GLU* 3.8 19.5 - - - +
119C ALA* 3.7 13.2 + - - +
203C LYS* 6.3 0.6 - - - +
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Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C PHE* 2.6 50.3 + - + +
113C ALA 2.6 13.1 + - - +
115C ARG* 1.3 91.2 + - - +
117C VAL* 1.3 58.0 + - - +
118C GLU 3.0 1.3 - - - -
119C ALA* 2.8 33.1 + - - +
120C LEU* 3.6 4.0 + - - +
196C PHE* 4.0 20.1 - - + -
199C LEU* 4.0 22.2 - - + -
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Residues in contact with VAL 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C MET* 4.6 4.3 - - - -
82C LEU* 3.7 30.1 - - + -
84C PHE* 4.8 2.9 - - + -
113C ALA 2.9 17.6 + - - +
114C VAL* 3.6 13.0 - - - +
116C GLN* 1.3 78.8 - - - +
118C GLU* 1.3 60.6 + - - +
120C LEU* 3.1 18.5 + - - +
121C ALA 3.5 3.8 + - - -
139C LEU* 4.1 6.2 - - + +
141C MET* 5.8 1.3 - - - -
162C VAL* 5.2 2.5 - - + -
185C PHE* 3.7 20.0 - - + -
189C VAL* 4.6 3.4 - - + -
196C PHE* 3.4 43.3 - - + -
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Residues in contact with GLU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLY* 3.1 13.2 - - - -
36C ARG* 2.7 62.6 + - - +
114C VAL 2.9 19.0 + - - +
115C ARG* 3.8 20.1 - - - +
116C GLN 3.0 0.2 - - - -
117C VAL* 1.3 73.5 - - - +
119C ALA* 1.3 59.2 + - - +
120C LEU 3.0 7.0 + - - -
121C ALA* 3.3 13.0 + - - +
137C GLY* 3.2 32.7 - - - +
138C ASN* 3.5 0.8 - - - -
139C LEU* 3.4 36.9 + - + -
141C MET* 4.1 2.2 - - + -
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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