Contacts of the helix formed by residues 108 - 125 (chain B) in PDB entry 1S13
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 THR 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B LEU* 5.4 1.3 - - + -
106B PRO* 4.4 13.2 - - + -
107B TYR* 1.3 70.3 - - - +
109B PRO* 1.3 64.7 - - + +
111B MET* 2.9 38.3 + - + +
112B GLN* 2.8 39.6 + - - +
216B GLU* 2.6 26.8 + - - +
220B LEU* 4.1 20.0 - - + -
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Residues in contact with PRO 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B TYR 4.7 0.2 - - - +
108B THR* 1.3 86.0 - - + +
110B ALA* 1.3 55.3 + - - +
112B GLN* 3.0 15.1 - - + +
113B ARG* 3.0 56.1 + - - +
216B GLU* 3.2 13.2 - - - +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B THR 3.2 0.2 - - - -
109B PRO* 1.3 75.9 - - - +
111B MET* 1.3 59.4 + - - +
113B ARG* 3.7 19.3 + - - +
114B TYR* 3.4 21.5 + - - +
209B LEU* 5.1 2.3 - - - +
212B GLN* 4.2 7.2 + - + +
213B LEU* 3.4 36.5 - - + +
216B GLU* 2.9 36.5 + - + +
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Residues in contact with MET 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 3.9 20.9 - - + +
53B SER* 3.3 36.8 - - - +
56B HIS* 3.8 16.8 - - + +
57B ILE* 5.6 3.3 - - + +
106B PRO* 3.5 26.5 - - + +
107B TYR* 3.9 12.3 - - + -
108B THR* 2.9 41.9 + - + +
110B ALA* 1.3 77.1 - - - +
112B GLN* 1.3 61.1 + - - +
114B TYR* 3.2 6.9 + - - +
115B VAL* 3.0 31.5 + - - +
213B LEU* 4.0 7.9 - - + -
217B LEU* 4.4 11.7 - - + -
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Residues in contact with GLN 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR* 3.3 60.3 + - + +
108B THR 2.8 12.3 + - - +
109B PRO* 2.9 39.5 - - + +
111B MET* 1.3 71.4 - - - +
113B ARG* 1.3 56.9 + - - +
115B VAL* 3.9 0.5 - - - +
116B LYS* 2.9 31.0 + - - +
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PRO* 3.0 49.9 + - - +
110B ALA* 3.7 12.9 - - - +
112B GLN* 1.3 76.2 - - - +
114B TYR* 1.3 65.4 + - - +
116B LYS* 3.5 5.2 + - - +
117B ARG* 3.0 24.6 + - - +
209B LEU* 4.6 7.8 - - + +
212B GLN* 2.7 49.7 + - - +
216B GLU* 4.5 3.2 + - - +
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 3.6 41.7 - - + -
110B ALA 3.4 9.0 + - - +
111B MET* 3.2 9.4 + - - +
113B ARG* 1.3 80.7 - - - +
115B VAL* 1.3 62.5 + - - +
117B ARG* 3.2 3.1 + - - +
118B LEU* 2.9 55.1 + - + +
132B HIS* 4.0 19.2 - + - -
135B THR* 4.7 6.1 + - - -
136B ARG* 3.4 20.6 + - + +
206B ALA* 4.3 5.2 + - - +
209B LEU* 4.0 37.4 - - + +
210B ASN* 2.9 39.1 + - - -
213B LEU* 4.5 7.0 - - + -
300B 2FH 4.8 0.2 - - - +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B HIS* 3.8 30.3 - - + +
57B ILE* 4.6 2.7 - - + +
60B ALA* 3.8 7.2 - - + -
107B TYR* 3.5 33.9 - - + +
111B MET 3.0 19.7 + - - +
112B GLN 3.9 0.7 - - - +
114B TYR* 1.3 75.6 - - + +
116B LYS* 1.3 65.7 + - - +
118B LEU* 2.8 22.3 + - - +
119B HIS* 3.0 35.9 + - + +
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLN 2.9 21.0 + - - +
113B ARG* 3.7 7.2 - - - +
115B VAL* 1.3 78.4 - - - +
117B ARG* 1.3 56.5 + - - +
119B HIS* 3.4 9.9 + - + +
120B GLU* 3.0 44.7 + - + +
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Residues in contact with ARG 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ARG 3.0 17.1 + - - +
114B TYR 3.5 4.9 - - - +
115B VAL 3.1 0.2 - - - -
116B LYS* 1.3 75.8 - - - +
118B LEU* 1.3 65.1 + - - +
120B GLU* 2.8 43.0 + - - +
121B VAL* 3.1 33.6 + - - +
125B GLU* 4.4 14.1 + - - -
128B LEU* 4.3 7.5 - - - +
132B HIS* 4.3 5.2 - - + +
202B GLU* 2.6 43.9 + - - +
205B THR* 4.7 7.5 - - + +
209B LEU* 4.1 22.9 - - + -
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 4.2 15.5 - - + +
60B ALA* 3.8 12.8 - - + +
61B LEU* 3.9 33.0 - - + +
64B GLU* 3.6 10.2 - - - +
114B TYR* 2.9 54.4 + - + +
115B VAL* 2.8 14.6 + - - +
117B ARG* 1.3 73.8 - - - +
119B HIS* 1.3 57.5 + - - +
121B VAL* 3.7 4.6 - - - +
122B GLY 3.0 22.9 + - - -
129B LEU* 4.5 5.5 - - + +
132B HIS* 3.4 40.6 - - + -
136B ARG* 6.5 0.4 - - + -
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Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ALA* 3.8 22.1 - - - +
63B GLU* 3.7 22.6 + - - -
64B GLU* 2.7 29.4 + - - +
67B ARG* 5.6 0.2 - - - -
115B VAL* 3.0 40.2 + - + +
116B LYS* 3.6 11.4 - - + +
118B LEU* 1.3 75.5 - - - +
120B GLU* 1.3 60.4 + - - +
123B ARG* 2.9 58.1 + - - +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LYS* 3.0 37.5 + - + +
117B ARG* 2.8 47.7 + - - +
119B HIS* 1.3 73.9 - - - +
121B VAL* 1.3 59.9 + - - +
123B ARG* 4.0 2.4 - - - +
124B THR* 2.9 40.5 + - - +
125B GLU* 5.4 1.3 - - - +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ARG* 3.1 39.7 + - - +
118B LEU* 3.7 7.2 - - - +
120B GLU* 1.3 76.0 - - - +
122B GLY* 1.3 64.2 + - - +
125B GLU* 2.8 56.8 + - + +
126B PRO 2.9 0.2 - - - -
128B LEU* 3.6 9.2 - - + +
129B LEU* 3.3 33.9 - - + +
132B HIS* 4.1 9.4 - - + +
202B GLU* 4.0 13.9 - - - +
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLU* 3.2 30.4 - - - +
67B ARG* 3.8 4.2 - - - -
68B ASN* 3.0 28.9 + - - +
118B LEU 3.0 12.8 + - - -
121B VAL* 1.3 81.0 - - - +
123B ARG* 1.3 59.5 + - - +
126B PRO* 4.1 4.8 - - - +
129B LEU* 4.3 8.5 - - - +
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU* 4.3 2.2 - - - -
67B ARG* 3.3 40.5 - - - +
119B HIS* 2.9 41.6 + - - +
120B GLU* 4.0 2.7 - - - +
122B GLY* 1.3 79.7 - - - +
124B THR* 1.3 69.4 + - + +
126B PRO* 4.7 2.6 - - - +
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU* 2.9 21.7 + - - +
123B ARG* 1.3 86.5 - - + +
125B GLU* 1.3 73.1 + - - +
126B PRO* 3.2 9.5 - - - +
127B GLU* 4.1 1.6 - - - +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ARG* 4.4 17.3 + - - -
120B GLU* 3.6 2.0 + - - +
121B VAL* 2.8 28.8 + - + +
124B THR* 1.3 90.6 + - - +
126B PRO* 1.3 55.9 - - - +
127B GLU* 2.9 16.6 - - - +
128B LEU* 2.9 34.6 + - + +
198B ARG* 2.5 30.8 + - - -
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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
------------------------------------------------------------
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