Contacts of the strand formed by residues 99 - 113 (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 GLU 99 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 3.2 33.3 + - + +
96C SER* 3.0 39.4 + - - +
98C ASP* 1.3 92.0 + - - +
100C VAL* 1.3 68.8 + - - +
134C TRP* 6.0 1.2 - - - -
135C TYR 3.5 4.9 - - - -
136C LYS* 3.5 37.7 + - - +
142C TRP* 4.0 0.4 - - - -
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Residues in contact with VAL 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 3.8 25.8 - - + -
19C LEU* 3.9 17.5 - - + -
92C TRP* 3.7 21.5 - - + -
93C GLU 3.6 11.9 - - - +
94C LYS* 4.1 7.4 - - + +
95C VAL* 4.2 1.5 - - - +
99C GLU* 1.3 84.4 - - - +
101C ILE* 1.3 77.3 + - - +
134C TRP* 3.7 2.3 - - - +
135C TYR* 2.9 33.3 + - + -
142C TRP* 3.4 28.7 - - + -
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Residues in contact with ILE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ARG 4.1 0.6 - - - +
92C TRP* 3.6 1.6 - - - -
93C GLU* 2.8 52.6 + - + +
95C VAL* 3.5 23.8 - - + -
100C VAL* 1.3 81.5 - - - +
102C GLY* 1.3 62.6 + - - +
103C TYR* 3.4 32.5 - - + +
132C LEU* 3.6 23.6 - - + -
133C HIS 3.4 2.5 - - - -
134C TRP* 4.0 28.7 - - + +
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Residues in contact with GLY 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ARG 3.7 4.7 - - - -
92C TRP* 3.7 21.5 - - - -
101C ILE* 1.3 76.4 - - - +
103C TYR* 1.3 64.1 + - - -
104C HIS* 3.8 11.4 - - - -
131C ASN 3.2 2.8 - - - +
132C LEU* 3.4 3.3 - - - -
133C HIS 2.7 38.8 + - - -
135C TYR* 4.0 1.6 - - - -
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Residues in contact with TYR 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.6 30.9 - + + +
37A ARG* 6.0 1.6 - - - -
90C THR* 3.1 6.8 - - - +
91C ARG* 2.8 76.5 + - + +
93C GLU* 3.8 22.4 + - + -
101C ILE* 3.4 27.7 - - + +
102C GLY* 1.3 71.4 - - - -
104C HIS* 1.3 60.3 + - - +
130C ALA* 6.3 1.6 - - + -
131C ASN 3.3 3.6 - - - -
132C LEU* 3.9 34.2 - - + +
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Residues in contact with HIS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 4.2 3.7 + - - -
23C VAL* 3.9 15.0 - - + +
87C ILE* 4.2 9.6 - - + +
89C GLY 3.5 4.0 - - - -
90C THR* 3.1 29.4 + - + +
92C TRP* 3.4 30.3 - + - -
102C GLY* 3.8 13.8 - - - -
103C TYR* 1.3 73.4 - - - +
105C GLN* 1.3 63.3 + - - +
106C LEU* 3.9 17.3 - - + -
130C ALA* 3.7 1.2 - - - -
131C ASN* 2.7 40.1 + - + +
133C HIS* 3.4 30.3 - + - +
135C TYR* 2.7 24.4 + - - -
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Residues in contact with GLN 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.8 14.8 - - + +
27A ALA* 3.8 12.4 - - - +
28A ASP* 4.8 8.0 + - + +
31A ASP* 4.2 9.5 + - - -
84A GLN* 4.9 4.0 - - - +
85A HIS 2.9 29.8 + - - -
86A PHE* 3.6 17.4 - - + +
87A ILE* 3.0 23.2 + - - +
88C GLY 3.0 22.2 + - - -
89C GLY* 2.7 47.5 + - - +
104C HIS* 1.3 73.2 - - - +
106C LEU* 1.3 67.6 + - - +
129C SER 3.5 6.7 - - - +
130C ALA* 4.8 2.0 - - + +
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 2.9 8.6 + - - +
86A PHE* 3.7 0.8 - - - -
26C TRP* 3.9 22.9 - - + -
85C HIS* 4.7 4.5 - - + -
86C PHE 3.4 14.8 - - - +
87C ILE* 4.3 14.6 - - + -
104C HIS* 3.9 19.5 - - + -
105C GLN* 1.3 84.5 - - - +
107C ARG* 1.3 59.5 + - - +
108C VAL* 4.0 13.5 - - + -
127C ALA 3.8 0.6 - - - +
128C HIS* 3.5 0.7 - - - -
129C SER* 2.7 53.2 + - - +
131C ASN* 3.5 27.4 - - + +
133C HIS* 5.1 1.6 - - + -
175C BFS 3.7 20.0 - - + -
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Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 3.5 15.5 - - - +
86A PHE* 3.7 15.3 - - + -
107A ARG* 3.1 27.0 - - - +
107B ARG* 3.3 44.2 - - - +
128B HIS* 4.8 1.2 + - - -
155B GLU* 4.4 1.0 + - - -
84C GLN* 3.3 4.0 + - - +
86C PHE* 3.2 36.3 + - + +
106C LEU* 1.3 71.2 - - - +
108C VAL* 1.3 63.0 + - - +
109C PRO* 3.4 31.8 - - - +
126C HIS* 3.4 30.1 + - + +
127C ALA 3.3 3.8 - - - +
128C HIS* 3.6 26.8 + - + +
155C GLU* 3.8 11.9 + - - -
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Residues in contact with VAL 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLN 3.1 11.9 - - - +
85C HIS* 3.7 39.5 - - + +
106C LEU* 4.0 11.4 - - + -
107C ARG* 1.3 77.2 - - - +
109C PRO* 1.3 59.5 - - - +
110C HIS* 3.2 35.4 + - + +
126C HIS* 3.4 1.1 - - - -
127C ALA 2.8 31.1 + - - +
175C BFS 3.6 33.4 - - + -
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Residues in contact with PRO 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B HIS* 3.8 20.4 - - + +
153B TRP* 3.8 10.0 - - + -
155B GLU* 5.0 0.9 - - - +
83C THR* 3.3 22.9 - - - -
84C GLN* 3.1 28.5 + - + +
107C ARG* 3.4 36.1 - - - +
108C VAL* 1.3 83.4 - - - +
110C HIS* 1.3 60.7 + - - +
126C HIS* 3.2 29.1 - - + +
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Residues in contact with HIS 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 4.2 3.6 - - + -
82C ARG 3.5 2.5 - - - -
83C THR* 3.2 27.5 - - + +
85C HIS* 4.7 5.3 + - - -
108C VAL* 3.2 35.5 + - + +
109C PRO* 1.3 73.3 - - - +
111C GLN* 1.3 64.4 + - - +
124C LYS* 3.4 5.2 - - - -
125C GLY 2.9 47.7 + - - +
126C HIS* 3.3 5.9 + - - -
158C PHE* 3.2 28.4 - + - -
161C ILE* 3.9 23.3 - - + -
162C PHE* 3.5 28.4 - + - -
175C BFS 3.6 7.2 + - - -
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Residues in contact with GLN 111 (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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153B TRP* 3.4 22.6 - - + -
154B GLY 3.2 17.2 + - - -
155B GLU* 3.8 10.8 - - - +
156B PHE 4.7 1.3 + - - +
80C THR 3.5 1.4 - - - +
81C LEU* 3.5 4.2 - - - +
82C ARG* 2.8 41.0 + - + +
110C HIS* 1.3 76.4 - - - +
112C ARG* 1.3 60.0 + - - +
113C TYR* 2.9 35.3 + - + -
121C VAL* 3.7 30.2 - - + +
123C MET 3.5 3.4 - - - +
124C LYS* 3.0 32.6 - - + +
126C HIS* 5.3 0.6 + - - +
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Residues in contact with ARG 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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73C LYS 5.5 0.6 + - - -
74C GLN* 4.9 5.7 + - - +
75C VAL 4.5 3.6 + - - -
78C ASP* 2.9 29.8 + - - +
80C THR* 3.2 8.0 + - - +
81C LEU* 3.4 42.9 - - + +
111C GLN* 1.3 71.1 - - - +
113C TYR* 1.3 58.4 + - - +
121C VAL* 3.5 6.4 - - - +
122C THR* 2.7 41.2 + - - +
123C MET* 2.9 46.2 + - + +
161C ILE* 3.1 32.0 + - + +
162C PHE* 4.4 8.1 - - - +
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Residues in contact with TYR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B TRP* 3.9 6.1 - - - +
154B GLY 3.6 10.2 + - - -
80C THR* 2.7 35.3 + - - +
82C ARG* 3.3 26.2 - - + -
111C GLN* 2.9 32.5 + - + -
112C ARG* 1.3 77.8 - - - +
114C LYS* 1.3 68.7 + - - +
115C ASP 3.8 16.4 - - - +
118C MET* 3.5 58.1 - - + +
119C LYS 5.5 0.2 - - - -
120C GLU 3.1 18.8 - - - +
121C VAL* 3.7 17.3 - - + -
122C THR* 3.7 7.5 + - - -
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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
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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