Contacts of the strand formed by residues 2102 - 2108 (chain C) in PDB entry 1W21
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 SER2102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2100C VAL* 3.3 9.3 - - - +
2101C ASN* 1.3 75.1 - - - +
2103C TRP* 1.3 66.1 + - - +
2368C TRP* 4.7 0.2 - - - -
2401C GLN* 3.6 7.8 + - - -
2457C SER* 2.7 30.0 + - - -
2459C LYS 2.9 24.0 - - - -
2460C ARG* 4.2 1.1 - - - -
2461C LEU* 2.9 43.9 + - - +
1G NAG 4.1 4.7 - - - +
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Residues in contact with TRP2103 (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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2100C VAL* 3.7 12.6 - - + -
2102C SER* 1.3 78.3 + - - +
2104C HIS* 1.3 60.8 + - - +
2361C PHE* 4.2 11.9 - + - -
2368C TRP* 3.2 54.3 - + + -
2383C MET* 3.6 31.1 - - + +
2401C GLN* 2.8 47.1 + - + +
2403C ILE* 4.7 0.9 - - + -
2428C PRO* 3.5 30.5 - - + -
2430C PHE* 3.5 30.3 - + + -
2454C LEU* 4.0 15.9 - - + +
2455C CYS* 3.4 21.5 - - - -
2456C GLY* 3.4 15.9 - - - -
2461C LEU* 4.5 8.0 - - - +
2462C GLY 5.1 2.1 - - - +
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Residues in contact with HIS2104 (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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209A SER* 5.7 1.6 - - - +
211A VAL* 3.6 21.6 - - + +
213A TRP* 5.2 0.2 - + - -
218A PRO* 3.7 32.9 - - + +
221A GLU* 3.9 19.2 + - + -
2102C SER 4.3 0.4 - - - -
2103C TRP* 1.3 73.3 - - - +
2105C ILE* 1.3 86.3 + - - +
2106C LEU* 4.4 5.4 - - + -
2427C ASN* 4.9 0.8 + - - -
2454C LEU* 3.1 9.4 - - - +
2455C CYS* 2.9 68.1 + - + +
2456C GLY 3.5 13.6 + - - -
2457C SER* 4.7 0.4 - - - -
2461C LEU* 3.5 24.5 - - + +
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Residues in contact with ILE2105 (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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183A ILE* 3.6 39.7 + - + +
202A SER* 3.7 21.1 - - - +
209A SER* 6.1 0.7 - - - +
211A VAL* 4.0 18.8 - - + +
213A TRP* 4.4 2.9 + - - -
2103C TRP 4.3 0.2 + - - -
2104C HIS* 1.3 88.1 + - - +
2106C LEU* 1.3 59.0 + - - +
2107C SER 3.9 6.7 - - - +
2108C LYS* 4.8 0.4 - - + -
2452C VAL* 3.6 30.5 - - + -
2453C ALA 3.6 11.7 - - - +
2454C LEU* 4.1 5.6 - - + +
2466C TRP* 3.5 37.4 - - + +
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Residues in contact with LEU2106 (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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180A VAL* 5.8 0.7 - - - +
182A CYS* 5.2 0.9 - - - -
183A ILE* 3.9 9.7 + - - +
213A TRP* 3.2 47.1 - - + -
218A PRO* 3.7 25.6 - - + -
2104C HIS* 3.5 2.4 + - + -
2105C ILE* 1.3 73.5 - - - +
2107C SER* 1.4 60.1 + - - +
2135C CYS* 5.7 4.3 - - - -
2169C MET* 3.9 24.6 - - + +
2416C PHE* 3.5 37.0 - - + -
2453C ALA* 2.8 25.8 + - + +
2454C LEU* 4.1 5.6 - - - -
2455C CYS* 3.8 17.9 - - - +
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Residues in contact with SER2107 (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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180A VAL* 5.1 1.5 - - - +
183A ILE* 3.6 12.8 - - - +
2105C ILE* 3.9 1.6 - - - +
2106C LEU* 1.4 83.2 - - - +
2108C LYS* 1.3 64.4 + - - +
2128C LEU* 5.0 0.2 - - - -
2137C MET* 3.3 10.0 - - - +
2169C MET* 3.3 26.2 - - - +
2170C GLY* 3.2 32.4 + - - -
2452C VAL* 3.5 3.1 - - - +
2453C ALA* 2.9 32.3 + - - +
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Residues in contact with LYS2108 (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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160A PRO 3.1 27.6 - - - +
161A PHE* 3.8 3.0 - - - -
180A VAL* 5.2 1.4 - - - +
183A ILE* 3.7 24.3 - - + +
2105C ILE* 4.8 0.7 - - + -
2107C SER* 1.3 79.7 + - - +
2109C ASP* 1.3 64.0 + - - +
2110C ASN* 2.7 39.3 + - - +
2137C MET* 4.6 0.9 - - - -
2170C GLY* 3.6 9.5 - - - +
2434C LEU* 4.6 3.7 - - - +
2450C SER* 4.8 1.0 + - - -
2451C ILE 3.3 15.0 - - - +
2452C VAL* 4.4 7.6 - - + -
2466C TRP* 3.8 30.1 - - + +
2467C HIS 2.9 29.3 + - - -
2468C ASP* 3.0 16.2 + - - +
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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