Contacts of the strand formed by residues 138 - 147 (chain K) in PDB entry 1S9C
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 CYS 138 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61K GLY* 4.6 10.3 - - - -
64K ILE* 4.7 6.3 - - - -
94K LEU* 4.3 3.6 - - + -
95K GLU 3.3 11.9 - - - +
96K LEU* 4.0 17.3 - - + -
97K TYR* 3.9 4.0 - - - -
100K LEU* 4.5 9.4 - - + -
106K LEU* 5.7 0.7 - - - -
128K VAL 4.2 0.2 - - - +
129K TYR* 3.7 2.4 - - - -
130K SER* 2.9 52.7 + - - +
136K LEU* 3.8 4.0 - - - +
137K ILE* 1.3 90.8 - - + +
139K HIS* 1.3 60.5 + - - +
140K ASN* 4.3 12.3 - - - -
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Residues in contact with HIS 139 (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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93K TYR* 3.8 23.6 - + - +
94K LEU* 3.4 5.6 - - - +
95K GLU* 3.0 33.0 + - + +
97K TYR* 3.5 28.9 + - + +
127K ASP* 2.9 29.4 + - - -
128K VAL 3.7 7.9 - - - -
129K TYR* 3.6 34.9 + + + +
138K CYS* 1.3 75.7 - - - +
140K ASN* 1.3 88.9 + - - +
141K GLN* 4.6 4.5 - - + -
162K LYS* 4.7 12.2 - - - -
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Residues in contact with ASN 140 (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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61K GLY 2.9 23.5 + - - -
62K VAL* 3.2 21.9 - - - +
65K GLY* 3.9 13.1 - - - +
92K GLN* 3.5 11.1 + - - +
93K TYR 3.4 2.5 - - - +
94K LEU* 3.3 16.9 - - - +
127K ASP* 3.5 0.7 - - - -
128K VAL* 2.9 42.0 + - + +
130K SER* 4.6 1.0 + - - -
138K CYS* 4.3 9.7 - - - -
139K HIS* 1.3 80.6 - - - +
141K GLN* 1.3 60.6 + - - +
142K PHE* 3.4 26.2 - - + -
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Residues in contact with GLN 141 (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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91K GLU 4.7 0.2 - - - -
92K GLN* 3.8 3.6 - - - -
93K TYR* 2.9 44.9 + - + +
125K ILE* 3.8 20.4 - - + +
126K MET 3.6 2.9 - - - +
127K ASP* 2.8 29.5 + - - +
139K HIS* 4.2 6.2 + - - +
140K ASN* 1.3 72.9 - - - +
142K PHE* 1.3 60.7 + - - +
143K SER* 3.6 5.5 + - - -
160K LYS 3.1 24.0 + - - -
161K VAL* 3.2 24.8 - - - +
162K LYS* 3.5 27.8 + - - +
243K LYS* 4.7 5.0 + - - -
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Residues in contact with PHE 142 (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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62K VAL* 3.5 17.9 - - + -
65K GLY 3.6 4.9 - - - -
66K GLN* 3.5 40.4 - - + -
89K HIS* 4.2 11.2 - + - +
92K GLN* 3.3 26.5 - - - -
124K ILE 4.0 0.5 - - - +
125K ILE* 3.7 2.3 - - - +
126K MET* 3.0 50.5 + - + +
128K VAL* 3.4 23.6 - - + -
140K ASN* 3.4 26.7 - - + -
141K GLN* 1.3 72.3 - - - +
143K SER* 1.3 59.8 + - - +
144K LEU* 3.8 17.0 + - + +
217K LEU* 4.6 4.0 - - + -
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Residues in contact with SER 143 (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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89K HIS* 3.6 4.7 - - - -
90K GLY* 2.9 26.9 + - - -
91K GLU* 3.1 51.2 + - - +
123K VAL* 4.1 16.6 - - - +
124K ILE 4.4 2.0 - - - -
125K ILE* 4.6 12.6 - - - +
141K GLN* 3.6 5.5 + - - -
142K PHE* 1.3 72.3 - - - +
144K LEU* 1.3 60.1 + - - +
161K VAL* 5.9 1.7 - - - +
243K LYS* 5.3 1.6 - - - -
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Residues in contact with LEU 144 (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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87K VAL* 3.7 22.7 - - + -
88K LEU 3.6 14.8 - - - +
89K HIS* 4.4 15.3 - - + -
90K GLY* 4.8 2.0 - - - -
122K VAL 4.1 2.2 - - - -
123K VAL* 3.2 29.0 - - - +
124K ILE* 3.2 42.3 + - + +
126K MET* 5.1 14.4 - - + -
142K PHE* 4.6 18.4 - - + +
143K SER* 1.3 79.0 + - - +
145K PHE* 1.3 62.8 + - - +
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Residues in contact with PHE 145 (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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87K VAL* 3.8 4.7 - - - -
88K LEU* 3.0 54.4 + - + +
90K GLY* 5.3 4.9 - - - +
118K LYS* 5.9 6.5 - - + -
120K SER* 4.6 8.1 - - - -
121K GLY* 4.0 20.0 - - - -
122K VAL 3.3 6.7 - - - -
123K VAL* 5.1 11.4 - - + -
124K ILE* 5.7 0.2 - - - -
144K LEU* 1.3 79.6 - - - +
146K LEU* 1.3 76.0 + - - +
147K VAL* 3.5 26.1 + - + -
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Residues in contact with LEU 146 (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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85K ALA* 4.4 9.4 - - + +
86K LYS 4.2 6.1 - - - +
87K VAL* 3.5 29.8 - - + -
121K GLY* 2.9 20.3 - - - -
122K VAL* 3.0 34.6 + - + -
124K ILE* 5.0 9.7 - - + +
145K PHE* 1.3 71.6 - - - +
147K VAL* 1.3 63.3 + - - +
148K GLY 2.9 11.8 + - - +
149K SER* 4.4 19.5 - - - +
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Residues in contact with VAL 147 (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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86K LYS* 2.9 73.6 + - + +
88K LEU* 4.2 18.2 - - + -
120K SER* 4.0 2.0 - - - -
145K PHE* 3.5 24.7 + - + +
146K LEU* 1.3 68.6 - - - +
148K GLY* 1.3 57.7 + - - +
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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