Contacts of the strand formed by residues 120 - 124 (chain B) in PDB entry 1CT8
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 SER 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B PRO 5.0 1.9 + - - -
119B PRO* 1.3 71.9 - - - +
121B VAL* 1.3 60.4 + - - +
122B TYR* 3.4 34.0 + - - -
141B LEU 3.4 2.4 - - - +
142B VAL* 3.7 0.5 - - - -
143B LYS* 2.9 40.6 + - - +
144B GLY 5.4 0.3 + - - -
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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
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123A GLU* 3.8 1.2 - - - +
119B PRO* 3.8 11.4 + - + +
120B SER* 1.3 76.3 - - - +
122B TYR* 1.3 71.0 + - - +
140B CYS* 4.5 2.2 - - - -
141B LEU 3.3 8.5 - - - +
142B VAL* 4.8 4.0 - - + -
195B CYS* 4.3 6.5 - - - -
197B VAL* 4.0 41.7 - - + -
206B VAL* 4.0 26.5 - - + -
208B LYS* 3.5 48.5 + - + +
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Residues in contact with TYR 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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121A SER* 3.9 19.1 - - - -
123A GLU* 4.1 10.8 - - + -
124A GLN* 3.7 56.9 + - + +
127A SER* 4.1 10.8 + - - -
120B SER* 3.4 38.1 + - - -
121B VAL* 1.3 82.7 - - - +
123B PRO* 1.3 69.2 - - + +
124B LEU* 5.0 2.7 - - + -
140B CYS* 3.4 3.6 - - - +
141B LEU* 2.8 60.2 + - + +
143B LYS* 4.2 11.6 - - + +
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Residues in contact with PRO 123 (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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121A SER* 3.7 21.0 - - - +
123A GLU* 3.7 31.6 - - + +
122B TYR* 1.3 86.9 - - + +
124B LEU* 1.3 61.1 - - - +
125B ALA* 3.9 3.4 + - + +
139B GLY 4.0 0.9 - - - +
140B CYS* 4.4 3.6 - - - -
208B LYS* 3.9 14.3 - - + -
209B LYS 3.7 22.2 - - - +
210B ILE* 3.8 19.5 - - + -
211B VAL* 5.4 4.9 - - + +
213B ARG* 4.8 2.3 + - - -
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Residues in contact with LEU 124 (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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118A PHE* 3.7 22.4 - - + +
119A PRO 4.8 7.6 - - - +
121A SER* 5.5 3.8 - - - +
131A SER 5.5 2.9 - - - +
133A VAL* 3.9 43.3 - - + -
135A PHE* 4.0 13.0 - - + -
122B TYR* 4.2 7.4 - - + +
123B PRO* 1.3 78.4 - - - +
125B ALA* 1.3 61.2 + - - +
138B LEU* 3.7 6.8 - - - -
139B GLY* 2.8 41.6 + - - +
140B CYS 3.7 22.4 - - - +
141B LEU* 4.1 13.9 - - + +
178B SER* 5.1 1.1 - - - -
210B ILE* 3.7 6.3 - - - +
213B ARG* 4.9 1.6 - - - +
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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