Contacts of the strand formed by residues 121 - 136 (chain C) in PDB entry 4STD
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 VAL 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B PHE 6.4 0.4 - - - +
111C GLN* 3.7 37.7 - - + +
112C ARG 3.5 6.1 - - - +
113C TYR* 3.7 24.5 - - + -
119C LYS 6.0 0.2 - - - -
120C GLU* 1.3 81.5 - - - +
122C THR* 1.3 63.7 + - - +
123C MET* 3.9 11.0 - - - +
124C LYS* 4.2 13.5 - - + -
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Residues in contact with THR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ARG* 2.7 32.9 + - - +
113C TYR 3.8 3.5 + - - -
114C LYS* 3.3 40.4 - - + +
120C GLU* 3.7 12.1 - - - +
121C VAL* 1.3 77.7 - - - +
123C MET* 1.3 67.4 + - - +
160C ARG* 5.0 1.0 + - - -
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Residues in contact with MET 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLN* 3.5 2.8 - - - -
112C ARG* 2.9 63.7 + - + +
121C VAL* 3.7 4.7 - - - +
122C THR* 1.3 88.4 + - - +
124C LYS* 1.3 64.3 + - - +
160C ARG* 3.4 62.1 - - + +
161C ILE* 3.9 15.1 - - + +
163C GLU* 5.4 2.9 - - - +
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Residues in contact with LYS 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLU* 2.7 36.1 + - - +
156B PHE* 3.6 26.9 - - - +
110C HIS 3.4 6.1 - - - +
111C GLN* 3.0 31.4 - - + +
121C VAL* 4.2 10.3 - - + -
123C MET* 1.3 78.3 - - - +
125C GLY* 1.3 59.2 + - - +
126C HIS* 4.0 5.2 - - - +
156C PHE* 3.4 31.9 - - + +
157C ASP* 2.9 28.9 + - - +
160C ARG* 4.6 1.3 + - - +
161C ILE* 3.9 5.7 - - - +
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Residues in contact with GLY 125 (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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110C HIS* 2.9 42.9 + - - +
124C LYS* 1.3 77.3 - - - +
126C HIS* 1.3 63.0 + - - +
155C GLU 3.6 4.7 - - - -
157C ASP 3.6 0.2 - - - -
158C PHE* 3.5 29.9 - - - -
161C ILE* 3.8 4.4 - - - +
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Residues in contact with HIS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B TRP* 5.4 2.2 - - - -
155B GLU* 2.9 40.2 + - - -
107C ARG* 3.4 25.7 + - - +
108C VAL 3.4 4.5 - - - +
109C PRO* 3.2 31.2 - - + +
110C HIS 3.3 14.6 + - - -
111C GLN* 5.3 1.2 + - - -
124C LYS* 4.0 7.2 - - + +
125C GLY* 1.3 77.5 - - - -
127C ALA* 1.3 60.2 + - - +
128C HIS* 3.4 5.8 - - + -
154C GLY* 3.1 3.9 - - - -
155C GLU* 2.7 46.3 + - + +
156C PHE* 3.3 27.8 - + - -
158C PHE* 4.6 1.1 - - - -
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Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU 3.8 0.7 - - - +
107C ARG* 3.3 5.0 - - - +
108C VAL* 2.8 36.9 + - - +
125C GLY 3.9 1.6 + - - -
126C HIS* 1.3 73.9 - - - +
128C HIS* 1.3 61.9 + - - +
129C SER* 4.1 0.7 - - - -
151C ILE* 3.8 19.3 - - + -
153C TRP 3.8 4.3 - - - -
154C GLY* 4.2 2.2 - - - -
158C PHE* 3.7 14.8 - - + -
175C BFS 3.2 33.7 - - + -
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Residues in contact with HIS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 3.4 33.4 - - + +
109A PRO* 3.9 14.7 - - + +
106C LEU 3.5 4.5 - - - -
107C ARG* 3.6 23.8 + - + +
126C HIS* 3.4 19.0 + - + -
127C ALA* 1.3 71.3 - - - +
129C SER* 1.3 61.6 + - - +
151C ILE* 3.8 1.4 - - - -
152C ARG* 3.0 25.6 + - + +
153C TRP* 2.9 73.2 + + - +
155C GLU* 3.8 15.2 + - + -
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Residues in contact with SER 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 3.8 5.0 + - - +
105C GLN* 3.5 3.8 - - - -
106C LEU* 2.7 50.8 + - - +
127C ALA 4.1 0.2 - - - -
128C HIS* 1.3 75.3 - - - +
130C ALA* 1.3 58.1 + - - +
131C ASN* 2.9 23.4 + - - -
150C ASP 3.2 22.9 - - - -
151C ILE* 3.7 13.5 - - - -
152C ARG* 4.5 6.7 - - - +
175C BFS 3.6 9.4 - - - -
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Residues in contact with ALA 130 (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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24A TYR* 4.1 9.2 - - - +
28A ASP* 4.0 10.5 - - - +
103C TYR* 6.3 1.6 - - + -
104C HIS 3.7 4.5 - - - -
105C GLN* 4.8 1.3 - - - +
129C SER* 1.3 72.0 - - - +
131C ASN* 1.3 62.8 + - - +
132C LEU 3.9 0.5 + - - -
148C LYS 3.8 2.1 - - - +
150C ASP* 2.9 34.1 + - + +
152C ARG* 3.4 36.3 - - - +
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Residues in contact with ASN 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 4.9 0.4 + - - -
102C GLY 3.2 5.4 - - - +
103C TYR* 3.3 4.3 - - - -
104C HIS* 2.7 46.7 + - + +
106C LEU* 3.5 18.5 - - + +
129C SER* 2.9 28.1 + - - -
130C ALA* 1.3 71.8 - - - +
132C LEU* 1.3 58.7 + - - +
133C HIS* 2.8 30.7 + - - +
147C LEU* 4.2 1.9 - - - +
148C LYS 3.9 1.1 - - - -
149C PRO* 3.5 25.1 - - - +
175C BFS 3.2 19.9 + - - -
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Residues in contact with LEU 132 (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 ILE* 3.6 28.5 - - + -
102C GLY 3.4 3.4 - - - -
103C TYR* 3.9 29.6 - - + +
130C ALA 3.9 1.2 + - - -
131C ASN* 1.3 71.9 - - - +
133C HIS* 1.3 65.4 + - - +
134C TRP* 3.7 39.0 - - + +
147C LEU* 3.3 2.1 - - - -
148C LYS* 2.7 60.0 + - + +
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Residues in contact with HIS 133 (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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23C VAL* 3.8 3.7 - - + +
26C TRP* 3.7 34.7 - + - -
101C ILE* 3.4 5.2 - - - -
102C GLY 2.7 30.6 + - - -
104C HIS* 3.4 17.4 - + - +
106C LEU* 5.1 1.8 - - + -
131C ASN* 2.8 32.0 + - + -
132C LEU* 1.3 86.1 - - - +
134C TRP* 1.3 64.9 + - - +
135C TYR* 3.0 35.2 + - + +
144C PHE* 3.6 16.4 - + + -
146C GLY 3.7 5.2 - - - +
147C LEU* 3.4 18.5 - - + +
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Residues in contact with TRP 134 (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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47C ARG* 3.5 59.5 - - + -
49C ASP* 4.4 5.2 - - + -
95C VAL* 6.1 0.4 - - + -
99C GLU* 6.0 1.1 - - - -
100C VAL 3.7 2.2 - - - -
101C ILE* 4.0 24.9 - - + +
132C LEU* 3.7 23.9 - - + +
133C HIS* 1.3 72.7 - - - +
135C TYR* 1.3 66.5 + - - +
136C LYS* 4.8 11.9 - - - +
144C PHE* 3.9 0.9 - - - -
145C ALA* 2.9 36.5 + - + +
146C GLY 3.2 11.1 + - - +
147C LEU* 3.6 33.9 - - - -
148C LYS* 3.9 22.0 - - + -
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Residues in contact with TYR 135 (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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19C LEU* 3.6 26.5 - - + -
22C CYS* 3.7 32.5 - - + -
23C VAL* 3.2 18.1 - - + +
92C TRP* 3.4 28.7 - + - -
99C GLU* 3.5 5.4 - - - -
100C VAL* 2.9 39.1 + - + +
102C GLY 4.0 1.8 - - - -
104C HIS* 2.7 24.1 + - - -
133C HIS* 3.0 37.5 + - + -
134C TRP* 1.3 78.7 - - - +
136C LYS* 1.3 70.0 + - - +
142C TRP* 4.0 6.5 - - + -
143C LYS 3.3 9.2 - - - +
144C PHE* 4.2 10.8 - + - -
145C ALA 4.3 0.2 - - - +
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Residues in contact with LYS 136 (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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43C ALA* 5.0 1.6 - - + -
98C ASP* 3.2 18.8 - - - +
99C GLU* 3.5 35.9 + - + +
134C TRP* 4.8 13.5 - - - +
135C TYR* 1.3 82.1 + - - +
137C LYS* 1.3 59.8 + - - +
138C ILE* 3.2 27.4 + - + -
142C TRP* 3.7 3.6 - - - -
143C LYS* 2.8 33.0 + - - +
145C ALA* 3.7 23.8 - - + +
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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
------------------------------------------------------------
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