Contacts of the strand formed by residues 107 - 114 (chain K) in PDB entry 3SDI
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 GLY 107 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76K VAL* 5.4 0.2 - - - +
103K GLY 3.9 1.0 - - - +
104K TYR* 3.7 14.4 - - - -
105K THR 2.9 28.9 + - - +
106K GLU* 1.3 83.7 - - - +
108K PRO* 1.3 75.7 - - - +
109K THR* 3.2 5.7 + - - -
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Residues in contact with PRO 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ARG* 3.1 47.3 + - + +
8K PHE 5.5 1.6 - - - +
11K GLY* 4.5 17.0 - - - +
12K ILE* 3.7 23.8 - - + -
103K GLY 3.5 7.6 - - - +
104K TYR* 3.5 20.5 - - + -
106K GLU 4.4 1.4 - - - +
107K GLY* 1.3 83.5 - - - +
109K THR* 1.3 61.1 + - - +
178K VAL* 5.2 2.7 - - + +
179K THR* 6.5 0.2 - - - -
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Residues in contact with THR 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ARG* 4.2 3.4 - - - +
12K ILE* 3.7 3.1 - - - +
76K VAL* 3.8 16.9 - - + +
101K ILE 3.8 1.2 - - - +
102K CYS* 3.4 3.3 - - - -
103K GLY 2.9 31.8 + - - -
106K GLU* 3.5 21.4 + - + +
107K GLY 3.2 10.4 + - - -
108K PRO* 1.3 78.4 + - - +
110K ILE* 1.3 66.4 + - - +
111K TYR* 3.5 28.9 - - + -
121K LYS* 3.9 28.1 - - + -
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Residues in contact with ILE 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K ALA* 3.7 15.9 - - + +
6K PHE* 3.7 11.0 - - - +
7K ARG* 3.6 21.4 - - - +
12K ILE* 4.1 19.3 - - + -
100K MET* 4.4 3.6 - - + -
101K ILE 3.6 2.7 - - - -
102K CYS* 4.0 17.9 - - - -
109K THR* 1.3 78.9 - - - +
111K TYR* 1.3 72.0 + - - +
121K LYS* 3.6 8.1 - - - +
122K GLY 3.3 37.1 + - - +
123K ASP 3.4 25.4 - - - +
124K ILE 4.7 0.2 - - - +
125K PHE* 3.7 21.5 - - + -
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Residues in contact with TYR 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLU* 4.2 4.2 + - - -
76K VAL* 3.7 18.2 - - + -
77K ALA* 3.5 29.9 - - + +
80K SER* 3.5 29.2 - - - -
100K MET* 3.1 6.8 - - - +
101K ILE* 2.8 41.0 + - - +
106K GLU* 5.1 0.2 + - - -
109K THR* 3.5 20.6 - - + +
110K ILE* 1.3 80.1 - - - +
112K TYR* 1.3 62.0 + - - +
113K VAL* 4.0 0.8 + - + -
119K ARG* 3.5 32.9 + - + -
120K LEU* 3.3 16.6 - - - -
121K LYS* 3.3 34.8 - - + +
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Residues in contact with TYR 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J ARG* 4.8 4.4 - - + +
27J LEU* 3.7 26.4 - - + +
98K GLY* 4.7 0.9 - - - -
99K THR 3.3 17.5 - - - -
100K MET* 4.3 3.1 - - + -
111K TYR* 1.3 73.3 - - - +
113K VAL* 1.3 59.6 + - - +
114K ASP* 2.8 45.3 + - + +
118K THR* 4.2 13.5 - - + -
119K ARG* 3.1 6.6 - - - +
120K LEU* 2.8 54.4 + - + +
125K PHE* 4.0 32.1 - + + -
127K VAL* 3.6 40.8 - - + +
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Residues in contact with VAL 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K SER* 3.9 34.3 - - - +
83K LEU* 4.2 13.2 - - + +
84K SER* 3.7 29.8 - - - +
87K VAL* 5.2 3.4 - - + -
97K MET* 6.5 0.4 - - + -
99K THR* 2.8 54.2 + - + -
101K ILE* 4.6 4.7 - - + -
111K TYR* 4.7 1.3 - - + -
112K TYR* 1.3 81.2 - - - +
114K ASP* 1.3 68.9 + - - +
118K THR 3.2 7.2 - - - +
119K ARG* 4.1 10.8 - - + -
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Residues in contact with ASP 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J ARG* 4.6 6.9 + - - +
87K VAL* 3.4 7.9 - - - +
97K MET* 3.2 15.7 - - - +
98K GLY* 4.3 3.1 - - - -
112K TYR* 2.8 32.4 + - + +
113K VAL* 1.3 77.1 - - - +
115K SER* 1.3 54.7 + - - +
116K ASP* 2.9 27.8 + - - +
117K GLY* 2.7 23.4 + - - -
118K THR* 3.0 35.1 + - - -
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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